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comparison FileFilter.xml @ 11:acf2b5b25c75 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 12:50:02 +0000
parents 348aec6301b1
children c8c4aa72a49d
comparison
equal deleted inserted replaced
10:05d5e1ddc985 11:acf2b5b25c75
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: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="FileFilter" name="FileFilter" version="2.3.0"> 4 <tool id="FileFilter" name="FileFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description> 5 <description>Extracts or manipulates portions of data from peak, feature or consensus-feature files.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">FileFilter</token> 7 <token name="@EXECUTABLE@">FileFilter</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[FileFilter 15 @EXT_FOO@
14 16 #import re
15 #if $param_in: 17
16 -in $param_in 18 ## Preprocessing
17 #end if 19 mkdir in &&
18 #if $param_out: 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 -out $param_out 21 mkdir out &&
20 #end if 22 #if $spectra.blackorwhitelist.file:
21 #if $param_out_type: 23 mkdir spectra.blackorwhitelist.file &&
22 -out_type 24 ln -s '$spectra.blackorwhitelist.file' 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)' &&
23 #if " " in str($param_out_type): 25 #end if
24 "$param_out_type" 26 #if $consensus.blackorwhitelist.file:
25 #else 27 mkdir consensus.blackorwhitelist.file &&
26 $param_out_type 28 ln -s '$consensus.blackorwhitelist.file' 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)' &&
27 #end if 29 #end if
28 #end if 30 #if $id.blacklist:
29 #if $param_rt: 31 mkdir id.blacklist &&
30 -rt "$param_rt" 32 ln -s '$id.blacklist' 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)' &&
31 #end if 33 #end if
32 #if $param_mz: 34
33 -mz "$param_mz" 35 ## Main program call
34 #end if 36
35 #if $param_int: 37 set -o pipefail &&
36 -int "$param_int" 38 @EXECUTABLE@ -write_ctd ./ &&
37 #end if 39 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
38 #if $param_sort: 40 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
39 -sort 41 -in
40 #end if 42 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
41 #if $param_peak_options_sn: 43 -out
42 -peak_options:sn $param_peak_options_sn 44 'out/output.${out_type}'
43 #end if 45 #if $spectra.blackorwhitelist.file:
44 46 -spectra:blackorwhitelist:file
45 #if $rep_param_peak_options_rm_pc_charge: 47 'spectra.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $spectra.blackorwhitelist.file.element_identifier)}.$gxy2omsext($spectra.blackorwhitelist.file.ext)'
46 -peak_options:rm_pc_charge 48 #end if
47 #for token in $rep_param_peak_options_rm_pc_charge: 49 #if $consensus.blackorwhitelist.file:
48 #if " " in str(token): 50 -consensus:blackorwhitelist:file
49 "$token.param_peak_options_rm_pc_charge" 51 'consensus.blackorwhitelist.file/${re.sub("[^\w\-_]", "_", $consensus.blackorwhitelist.file.element_identifier)}.$gxy2omsext($consensus.blackorwhitelist.file.ext)'
50 #else 52 #end if
51 $token.param_peak_options_rm_pc_charge 53 #if $id.blacklist:
52 #end if 54 -id:blacklist
53 #end for 55 'id.blacklist/${re.sub("[^\w\-_]", "_", $id.blacklist.element_identifier)}.$gxy2omsext($id.blacklist.ext)'
54 #end if 56 #end if
55 #if $param_peak_options_pc_mz_range: 57
56 -peak_options:pc_mz_range "$param_peak_options_pc_mz_range" 58 ## Postprocessing
57 #end if 59 && mv 'out/output.${out_type}' '$out'
58 60 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
59 #if $rep_param_peak_options_pc_mz_list: 61 && mv '@EXECUTABLE@.ctd' '$ctd_out'
60 -peak_options:pc_mz_list 62 #end if]]></command>
61 #for token in $rep_param_peak_options_pc_mz_list: 63 <configfiles>
62 #if " " in str(token): 64 <inputs name="args_json" data_style="paths"/>
63 "$token.param_peak_options_pc_mz_list" 65 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
64 #else 66 </configfiles>
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 $param_peak_options_mz_precision:
90 -peak_options:mz_precision
91 #if " " in str($param_peak_options_mz_precision):
92 "$param_peak_options_mz_precision"
93 #else
94 $param_peak_options_mz_precision
95 #end if
96 #end if
97 #if $param_peak_options_int_precision:
98 -peak_options:int_precision
99 #if " " in str($param_peak_options_int_precision):
100 "$param_peak_options_int_precision"
101 #else
102 $param_peak_options_int_precision
103 #end if
104 #end if
105 #if $param_peak_options_indexed_file:
106 -peak_options:indexed_file
107 #end if
108 #if $param_peak_options_zlib_compression:
109 -peak_options:zlib_compression
110 #end if
111 #if $param_peak_options_numpress_masstime:
112 -peak_options:numpress:masstime
113 #if " " in str($param_peak_options_numpress_masstime):
114 "$param_peak_options_numpress_masstime"
115 #else
116 $param_peak_options_numpress_masstime
117 #end if
118 #end if
119 #if $param_peak_options_numpress_masstime_error:
120 -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error
121 #end if
122 #if $param_peak_options_numpress_intensity:
123 -peak_options:numpress:intensity
124 #if " " in str($param_peak_options_numpress_intensity):
125 "$param_peak_options_numpress_intensity"
126 #else
127 $param_peak_options_numpress_intensity
128 #end if
129 #end if
130 #if $param_peak_options_numpress_intensity_error:
131 -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error
132 #end if
133 #if $param_spectra_remove_zoom:
134 -spectra:remove_zoom
135 #end if
136 #if $param_spectra_remove_mode:
137 -spectra:remove_mode
138 #if " " in str($param_spectra_remove_mode):
139 "$param_spectra_remove_mode"
140 #else
141 $param_spectra_remove_mode
142 #end if
143 #end if
144 #if $param_spectra_remove_activation:
145 -spectra:remove_activation
146 #if " " in str($param_spectra_remove_activation):
147 "$param_spectra_remove_activation"
148 #else
149 $param_spectra_remove_activation
150 #end if
151 #end if
152 #if $param_spectra_remove_collision_energy:
153 -spectra:remove_collision_energy "$param_spectra_remove_collision_energy"
154 #end if
155 #if $param_spectra_remove_isolation_window_width:
156 -spectra:remove_isolation_window_width "$param_spectra_remove_isolation_window_width"
157 #end if
158 #if $param_spectra_select_zoom:
159 -spectra:select_zoom
160 #end if
161 #if $param_spectra_select_mode:
162 -spectra:select_mode
163 #if " " in str($param_spectra_select_mode):
164 "$param_spectra_select_mode"
165 #else
166 $param_spectra_select_mode
167 #end if
168 #end if
169 #if $param_spectra_select_activation:
170 -spectra:select_activation
171 #if " " in str($param_spectra_select_activation):
172 "$param_spectra_select_activation"
173 #else
174 $param_spectra_select_activation
175 #end if
176 #end if
177 #if $param_spectra_select_collision_energy:
178 -spectra:select_collision_energy "$param_spectra_select_collision_energy"
179 #end if
180 #if $param_spectra_select_isolation_window_width:
181 -spectra:select_isolation_window_width "$param_spectra_select_isolation_window_width"
182 #end if
183 #if $param_spectra_select_polarity:
184 -spectra:select_polarity
185 #if " " in str($param_spectra_select_polarity):
186 "$param_spectra_select_polarity"
187 #else
188 $param_spectra_select_polarity
189 #end if
190 #end if
191 #if $param_feature_q:
192 -feature:q "$param_feature_q"
193 #end if
194
195 #if $rep_param_consensus_map:
196 -consensus:map
197 #for token in $rep_param_consensus_map:
198 #if " " in str(token):
199 "$token.param_consensus_map"
200 #else
201 $token.param_consensus_map
202 #end if
203 #end for
204 #end if
205 #if $param_consensus_map_and:
206 -consensus:map_and
207 #end if
208 #if $param_consensus_blackorwhitelist_blacklist:
209 -consensus:blackorwhitelist:blacklist
210 #if " " in str($param_consensus_blackorwhitelist_blacklist):
211 "$param_consensus_blackorwhitelist_blacklist"
212 #else
213 $param_consensus_blackorwhitelist_blacklist
214 #end if
215 #end if
216 #if $param_consensus_blackorwhitelist_file:
217 -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file
218 #end if
219
220 #if $rep_param_consensus_blackorwhitelist_maps:
221 -consensus:blackorwhitelist:maps
222 #for token in $rep_param_consensus_blackorwhitelist_maps:
223 #if " " in str(token):
224 "$token.param_consensus_blackorwhitelist_maps"
225 #else
226 $token.param_consensus_blackorwhitelist_maps
227 #end if
228 #end for
229 #end if
230 #if $param_consensus_blackorwhitelist_rt:
231 -consensus:blackorwhitelist:rt $param_consensus_blackorwhitelist_rt
232 #end if
233 #if $param_consensus_blackorwhitelist_mz:
234 -consensus:blackorwhitelist:mz $param_consensus_blackorwhitelist_mz
235 #end if
236 #if $param_consensus_blackorwhitelist_use_ppm_tolerance:
237 -consensus:blackorwhitelist:use_ppm_tolerance
238 #end if
239 #if $param_f_and_c_charge:
240 -f_and_c:charge "$param_f_and_c_charge"
241 #end if
242 #if $param_f_and_c_size:
243 -f_and_c:size "$param_f_and_c_size"
244 #end if
245
246 #if $rep_param_f_and_c_remove_meta:
247 -f_and_c:remove_meta
248 #for token in $rep_param_f_and_c_remove_meta:
249 #if " " in str(token):
250 "$token.param_f_and_c_remove_meta"
251 #else
252 $token.param_f_and_c_remove_meta
253 #end if
254 #end for
255 #end if
256 #if $param_id_keep_best_score_id:
257 -id:keep_best_score_id
258 #end if
259
260 #if $rep_param_id_sequences_whitelist:
261 -id:sequences_whitelist
262 #for token in $rep_param_id_sequences_whitelist:
263 #if " " in str(token):
264 "$token.param_id_sequences_whitelist"
265 #else
266 $token.param_id_sequences_whitelist
267 #end if
268 #end for
269 #end if
270
271 #if $rep_param_id_accessions_whitelist:
272 -id:accessions_whitelist
273 #for token in $rep_param_id_accessions_whitelist:
274 #if " " in str(token):
275 "$token.param_id_accessions_whitelist"
276 #else
277 $token.param_id_accessions_whitelist
278 #end if
279 #end for
280 #end if
281 #if $param_id_remove_annotated_features:
282 -id:remove_annotated_features
283 #end if
284 #if $param_id_remove_unannotated_features:
285 -id:remove_unannotated_features
286 #end if
287 #if $param_id_remove_unassigned_ids:
288 -id:remove_unassigned_ids
289 #end if
290 #if $param_id_blacklist:
291 -id:blacklist $param_id_blacklist
292 #end if
293 #if $param_id_rt:
294 -id:rt $param_id_rt
295 #end if
296 #if $param_id_mz:
297 -id:mz $param_id_mz
298 #end if
299 #if $param_id_blacklist_imperfect:
300 -id:blacklist_imperfect
301 #end if
302 #if $param_algorithm_SignalToNoise_win_len:
303 -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
304 #end if
305 #if $param_algorithm_SignalToNoise_bin_count:
306 -algorithm:SignalToNoise:bin_count $param_algorithm_SignalToNoise_bin_count
307 #end if
308 #if $param_algorithm_SignalToNoise_min_required_elements:
309 -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
310 #end if
311 #if $param_algorithm_SignalToNoise_write_log_messages:
312 -algorithm:SignalToNoise:write_log_messages
313 #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
314 "$param_algorithm_SignalToNoise_write_log_messages"
315 #else
316 $param_algorithm_SignalToNoise_write_log_messages
317 #end if
318 #end if
319 #if $adv_opts.adv_opts_selector=='advanced':
320 #if $adv_opts.param_force:
321 -force
322 #end if
323 #if $adv_opts.param_id_remove_clashes:
324 -id:remove_clashes
325 #end if
326 #if $adv_opts.param_algorithm_SignalToNoise_max_intensity:
327 -algorithm:SignalToNoise:max_intensity $adv_opts.param_algorithm_SignalToNoise_max_intensity
328 #end if
329 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor:
330 -algorithm:SignalToNoise:auto_max_stdev_factor $adv_opts.param_algorithm_SignalToNoise_auto_max_stdev_factor
331 #end if
332 #if $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile:
333 -algorithm:SignalToNoise:auto_max_percentile $adv_opts.param_algorithm_SignalToNoise_auto_max_percentile
334 #end if
335 #if $adv_opts.param_algorithm_SignalToNoise_auto_mode:
336 -algorithm:SignalToNoise:auto_mode $adv_opts.param_algorithm_SignalToNoise_auto_mode
337 #end if
338 #if $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window:
339 -algorithm:SignalToNoise:noise_for_empty_window $adv_opts.param_algorithm_SignalToNoise_noise_for_empty_window
340 #end if
341 #end if
342 ]]></command>
343 <inputs> 67 <inputs>
344 <param name="param_in" type="data" format="mzml,featurexml,consensusxml" optional="False" label="Input file" help="(-in) "/> 68 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,mzml" optional="false" label="Input file" help=" select consensusxml,featurexml,mzml data sets(s)"/>
345 <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) "> 69 <param name="out_type" argument="-out_type" display="radio" type="select" optional="false" label="Output file type -- default: determined from file extension or content" help="">
346 <option value="mzML">mzML</option> 70 <option value="consensusXML">consensusxml</option>
347 <option value="featureXML">featureXML</option> 71 <option value="featureXML">featurexml</option>
348 <option value="consensusXML">consensusXML</option> 72 <option value="mzML">mzml</option>
349 </param> 73 <expand macro="list_string_san"/>
350 <param name="param_rt" type="text" size="30" value=":" label="Retention time range to extract" help="(-rt) "> 74 </param>
351 <sanitizer> 75 <param name="rt" argument="-rt" type="text" optional="true" value=":" label="Retention time range to extract" help="">
352 <valid initial="string.printable"> 76 <expand macro="list_string_san"/>
353 <remove value="'"/> 77 </param>
354 <remove value="&quot;"/> 78 <param name="mz" argument="-mz" type="text" optional="true" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="">
355 </valid> 79 <expand macro="list_string_san"/>
356 </sanitizer> 80 </param>
357 </param> 81 <param name="int" argument="-int" type="text" optional="true" value=":" label="Intensity range to extract" help="">
358 <param name="param_mz" type="text" size="30" value=":" label="m/z range to extract (applies to ALL ms levels!)" help="(-mz) "> 82 <expand macro="list_string_san"/>
359 <sanitizer> 83 </param>
360 <valid initial="string.printable"> 84 <param name="sort" argument="-sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the output according to RT and m/z" help=""/>
361 <remove value="'"/> 85 <section name="peak_options" title="Peak data options" help="" expanded="false">
362 <remove value="&quot;"/> 86 <param name="sn" argument="-peak_options:sn" type="float" optional="true" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help=""/>
363 </valid> 87 <param name="rm_pc_charge" argument="-peak_options:rm_pc_charge" type="text" optional="true" value="" label="Remove MS(2) spectra with these precursor charges" help="All spectra without precursor are kept! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
364 </sanitizer> 88 <expand macro="list_integer_valsan"/>
365 </param> 89 </param>
366 <param name="param_int" type="text" size="30" value=":" label="Intensity range to extract" help="(-int) "> 90 <param name="pc_mz_range" argument="-peak_options:pc_mz_range" type="text" optional="true" value=":" label="MSn (n&gt;=2) precursor filtering according to their m/z value" help="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">
367 <sanitizer> 91 <expand macro="list_string_san"/>
368 <valid initial="string.printable"> 92 </param>
369 <remove value="'"/> 93 <param name="pc_mz_list" argument="-peak_options:pc_mz_list" type="text" optional="true" value="" label="List of m/z values" help="If a precursor window covers ANY of these values, the corresponding MS/MS spectrum will be kept (space separated list, in order to allow for spaces in list items surround them by single quotes)">
370 <remove value="&quot;"/> 94 <expand macro="list_float_valsan"/>
371 </valid> 95 </param>
372 </sanitizer> 96 <param name="level" argument="-peak_options:level" type="text" optional="true" value="1 2 3" label="MS levels to extract" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
373 </param> 97 <expand macro="list_integer_valsan"/>
374 <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) "/> 98 </param>
375 <param name="param_peak_options_sn" type="float" value="0.0" label="Write peaks with S/N &gt; 'sn' values only" help="(-sn) "/> 99 <param name="sort_peaks" argument="-peak_options:sort_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sorts the peaks according to m/z" help=""/>
376 <repeat name="rep_param_peak_options_rm_pc_charge" min="0" title="param_peak_options_rm_pc_charge"> 100 <param name="no_chromatograms" argument="-peak_options:no_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="No conversion to space-saving real chromatograms" help="e.g. from SRM scans"/>
377 <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!"> 101 <param name="remove_chromatograms" argument="-peak_options:remove_chromatograms" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes chromatograms stored in a file" help=""/>
378 <sanitizer> 102 <param name="remove_empty" argument="-peak_options:remove_empty" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Removes spectra and chromatograms without peaks" help=""/>
379 <valid initial="string.printable"> 103 <param name="mz_precision" argument="-peak_options:mz_precision" display="radio" type="select" optional="false" label="Store base64 encoded m/z data using 32 or 64 bit precision" help="">
380 <remove value="'"/> 104 <option value="32">32</option>
381 <remove value="&quot;"/> 105 <option value="64" selected="true">64</option>
382 </valid> 106 <expand macro="list_string_san"/>
383 </sanitizer> 107 </param>
384 </param> 108 <param name="int_precision" argument="-peak_options:int_precision" display="radio" type="select" optional="false" label="Store base64 encoded intensity data using 32 or 64 bit precision" help="">
385 </repeat> 109 <option value="32" selected="true">32</option>
386 <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"> 110 <option value="64">64</option>
387 <sanitizer> 111 <expand macro="list_string_san"/>
388 <valid initial="string.printable"> 112 </param>
389 <remove value="'"/> 113 <param name="indexed_file" argument="-peak_options:indexed_file" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to add an index to the file when writing" help=""/>
390 <remove value="&quot;"/> 114 <param name="zlib_compression" argument="-peak_options:zlib_compression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Whether to store data with zlib compression (lossless compression)" help=""/>
391 </valid> 115 <section name="numpress" title="Numpress compression for peak data" help="" expanded="false">
392 </sanitizer> 116 <param name="masstime" argument="-peak_options:numpress:masstime" display="radio" type="select" optional="false" label="Apply MS Numpress compression algorithms in m/z or rt dimension (recommended: linear)" help="">
393 </param> 117 <option value="none" selected="true">none</option>
394 <repeat name="rep_param_peak_options_pc_mz_list" min="0" title="param_peak_options_pc_mz_list"> 118 <option value="linear">linear</option>
395 <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"> 119 <option value="pic">pic</option>
396 <sanitizer> 120 <option value="slof">slof</option>
397 <valid initial="string.printable"> 121 <expand macro="list_string_san"/>
398 <remove value="'"/> 122 </param>
399 <remove value="&quot;"/> 123 <param name="lossy_mass_accuracy" argument="-peak_options:numpress:lossy_mass_accuracy" type="float" optional="true" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression" help="(e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
400 </valid> 124 <param name="intensity" argument="-peak_options:numpress:intensity" display="radio" type="select" optional="false" label="Apply MS Numpress compression algorithms in intensity dimension (recommended: slof or pic)" help="">
401 </sanitizer> 125 <option value="none" selected="true">none</option>
402 </param> 126 <option value="linear">linear</option>
403 </repeat> 127 <option value="pic">pic</option>
404 <repeat name="rep_param_peak_options_level" min="0" max="1" title="param_peak_options_level"> 128 <option value="slof">slof</option>
405 <param name="param_peak_options_level" type="text" size="30" value="1 2 3" label="MS levels to extract" help="(-level) "> 129 <expand macro="list_string_san"/>
406 <sanitizer> 130 </param>
407 <valid initial="string.printable"> 131 <param name="float_da" argument="-peak_options:numpress:float_da" display="radio" type="select" optional="false" label="Apply MS Numpress compression algorithms for the float data arrays (recommended: slof or pic)" help="">
408 <remove value="'"/> 132 <option value="none" selected="true">none</option>
409 <remove value="&quot;"/> 133 <option value="linear">linear</option>
410 </valid> 134 <option value="pic">pic</option>
411 </sanitizer> 135 <option value="slof">slof</option>
412 </param> 136 <expand macro="list_string_san"/>
413 </repeat> 137 </param>
414 <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) "/> 138 </section>
415 <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"/> 139 </section>
416 <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) "/> 140 <section name="spectra" title="Remove spectra or select spectra (removing all others) with certain properties" help="" expanded="false">
417 <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) "> 141 <param name="remove_zoom" argument="-spectra:remove_zoom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove zoom (enhanced resolution) scans" help=""/>
418 <option value="32">32</option> 142 <param name="remove_mode" argument="-spectra:remove_mode" type="select" optional="true" label="Remove scans by scan mode" help="">
419 <option value="64" selected="true">64</option> 143 <option value="">default (nothing chosen)</option>
420 </param> 144 <option value="Unknown">Unknown</option>
421 <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) "> 145 <option value="MassSpectrum">MassSpectrum</option>
422 <option value="32" selected="true">32</option> 146 <option value="MS1Spectrum">MS1Spectrum</option>
423 <option value="64">64</option> 147 <option value="MSnSpectrum">MSnSpectrum</option>
424 </param> 148 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
425 <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) "/> 149 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
426 <param name="param_peak_options_zlib_compression" display="radio" type="boolean" truevalue="-peak_options:zlib_compression" falsevalue="" checked="false" optional="True" label="Whether to store data with zlib compression (lossless compression)" help="(-zlib_compression) "/> 150 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
427 <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) "> 151 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
428 <option value="none" selected="true">none</option> 152 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
429 <option value="linear">linear</option> 153 <option value="Precursor">Precursor</option>
430 <option value="pic">pic</option> 154 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
431 <option value="slof">slof</option> 155 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
432 </param> 156 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
433 <param name="param_peak_options_numpress_masstime_error" type="float" value="0.0001" label="Maximal allowable error in m/z or rt dimension (default 10 ppm at 100 m/z; set to 0.5 for pic or negative to disable check and speed up conversion)" help="(-masstime_error) "/> 157 <option value="Emission">Emission</option>
434 <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) "> 158 <option value="Absorption">Absorption</option>
435 <option value="none" selected="true">none</option> 159 <expand macro="list_string_san"/>
436 <option value="linear">linear</option> 160 </param>
437 <option value="pic">pic</option> 161 <param name="remove_activation" argument="-spectra:remove_activation" type="select" optional="true" label="Remove MSn scans where any of its precursors features a certain activation method" help="">
438 <option value="slof">slof</option> 162 <option value="">default (nothing chosen)</option>
439 </param> 163 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
440 <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 or negative to disable check and speed up conversion)" help="(-intensity_error) "/> 164 <option value="Post-source decay">Post-source decay</option>
441 <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) "/> 165 <option value="Plasma desorption">Plasma desorption</option>
442 <param name="param_spectra_remove_mode" type="select" optional="True" label="Remove scans by scan mode" help="(-remove_mode) "> 166 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
443 <option value="Unknown">Unknown</option> 167 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
444 <option value="MassSpectrum">MassSpectrum</option> 168 <option value="Electron capture dissociation">Electron capture dissociation</option>
445 <option value="MS1Spectrum">MS1Spectrum</option> 169 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
446 <option value="MSnSpectrum">MSnSpectrum</option> 170 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
447 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option> 171 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
448 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option> 172 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
449 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option> 173 <option value="Photodissociation">Photodissociation</option>
450 <option value="ConstantNeutralGain">ConstantNeutralGain</option> 174 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
451 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option> 175 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
452 <option value="Precursor">Precursor</option> 176 <expand macro="list_string_san"/>
453 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> 177 </param>
454 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> 178 <param name="remove_collision_energy" argument="-spectra:remove_collision_energy" type="text" optional="true" value=":" label="Remove MSn scans with a collision energy in the given interval" help="">
455 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> 179 <expand macro="list_string_san"/>
456 <option value="Emission">Emission</option> 180 </param>
457 <option value="Absorption">Absorption</option> 181 <param name="remove_isolation_window_width" argument="-spectra:remove_isolation_window_width" type="text" optional="true" value=":" label="Remove MSn scans whose isolation window width is in the given interval" help="">
458 </param> 182 <expand macro="list_string_san"/>
459 <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) "> 183 </param>
460 <option value="Collision-induced dissociation">Collision-induced dissociation</option> 184 <param name="select_zoom" argument="-spectra:select_zoom" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Select zoom (enhanced resolution) scans" help=""/>
461 <option value="Post-source decay">Post-source decay</option> 185 <param name="select_mode" argument="-spectra:select_mode" type="select" optional="true" label="Selects scans by scan mode." help="">
462 <option value="Plasma desorption">Plasma desorption</option> 186 <option value="">default (nothing chosen)</option>
463 <option value="Surface-induced dissociation">Surface-induced dissociation</option> 187 <option value="Unknown">Unknown</option>
464 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> 188 <option value="MassSpectrum">MassSpectrum</option>
465 <option value="Electron capture dissociation">Electron capture dissociation</option> 189 <option value="MS1Spectrum">MS1Spectrum</option>
466 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> 190 <option value="MSnSpectrum">MSnSpectrum</option>
467 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> 191 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option>
468 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> 192 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option>
469 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> 193 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option>
470 <option value="Photodissociation">Photodissociation</option> 194 <option value="ConstantNeutralGain">ConstantNeutralGain</option>
471 <option value="Electron transfer dissociation">Electron transfer dissociation</option> 195 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option>
472 <option value="Pulsed q dissociation">Pulsed q dissociation</option> 196 <option value="Precursor">Precursor</option>
473 </param> 197 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option>
474 <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) "> 198 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option>
475 <sanitizer> 199 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option>
476 <valid initial="string.printable"> 200 <option value="Emission">Emission</option>
477 <remove value="'"/> 201 <option value="Absorption">Absorption</option>
478 <remove value="&quot;"/> 202 <expand macro="list_string_san"/>
479 </valid> 203 </param>
480 </sanitizer> 204 <param name="select_activation" argument="-spectra:select_activation" type="select" optional="true" label="Retain MSn scans where any of its precursors features a certain activation method" help="">
481 </param> 205 <option value="">default (nothing chosen)</option>
482 <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) "> 206 <option value="Collision-induced dissociation">Collision-induced dissociation</option>
483 <sanitizer> 207 <option value="Post-source decay">Post-source decay</option>
484 <valid initial="string.printable"> 208 <option value="Plasma desorption">Plasma desorption</option>
485 <remove value="'"/> 209 <option value="Surface-induced dissociation">Surface-induced dissociation</option>
486 <remove value="&quot;"/> 210 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option>
487 </valid> 211 <option value="Electron capture dissociation">Electron capture dissociation</option>
488 </sanitizer> 212 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option>
489 </param> 213 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option>
490 <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) "/> 214 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option>
491 <param name="param_spectra_select_mode" type="select" optional="True" label="Selects scans by scan mode" help="(-select_mode) "> 215 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
492 <option value="Unknown">Unknown</option> 216 <option value="Photodissociation">Photodissociation</option>
493 <option value="MassSpectrum">MassSpectrum</option> 217 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
494 <option value="MS1Spectrum">MS1Spectrum</option> 218 <option value="Pulsed q dissociation">Pulsed q dissociation</option>
495 <option value="MSnSpectrum">MSnSpectrum</option> 219 <expand macro="list_string_san"/>
496 <option value="SelectedIonMonitoring">SelectedIonMonitoring</option> 220 </param>
497 <option value="SelectedReactionMonitoring">SelectedReactionMonitoring</option> 221 <param name="select_collision_energy" argument="-spectra:select_collision_energy" type="text" optional="true" value=":" label="Select MSn scans with a collision energy in the given interval" help="">
498 <option value="ConsecutiveReactionMonitoring">ConsecutiveReactionMonitoring</option> 222 <expand macro="list_string_san"/>
499 <option value="ConstantNeutralGain">ConstantNeutralGain</option> 223 </param>
500 <option value="ConstantNeutralLoss">ConstantNeutralLoss</option> 224 <param name="select_isolation_window_width" argument="-spectra:select_isolation_window_width" type="text" optional="true" value=":" label="Select MSn scans whose isolation window width is in the given interval" help="">
501 <option value="Precursor">Precursor</option> 225 <expand macro="list_string_san"/>
502 <option value="EnhancedMultiplyCharged">EnhancedMultiplyCharged</option> 226 </param>
503 <option value="TimeDelayedFragmentation">TimeDelayedFragmentation</option> 227 <param name="select_polarity" argument="-spectra:select_polarity" display="radio" type="select" optional="true" label="Retain MSn scans with a certain scan polarity" help="">
504 <option value="ElectromagneticRadiation">ElectromagneticRadiation</option> 228 <option value="">default (nothing chosen)</option>
505 <option value="Emission">Emission</option> 229 <option value="unknown">unknown</option>
506 <option value="Absorption">Absorption</option> 230 <option value="positive">positive</option>
507 </param> 231 <option value="negative">negative</option>
508 <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) "> 232 <expand macro="list_string_san"/>
509 <option value="Collision-induced dissociation">Collision-induced dissociation</option> 233 </param>
510 <option value="Post-source decay">Post-source decay</option> 234 <section name="blackorwhitelist" title="Black or white listing of of MS2 spectra by spectral similarity" help="" expanded="false">
511 <option value="Plasma desorption">Plasma desorption</option> 235 <param name="file" argument="-spectra:blackorwhitelist:file" type="data" format="mzml" optional="true" label="Input file containing MS2 spectra that should be retained or removed from the mzML file" help="Matching tolerances are taken from 'spectra:blackorwhitelist:similarity_threshold|rt|mz' options.. select mzml data sets(s)"/>
512 <option value="Surface-induced dissociation">Surface-induced dissociation</option> 236 <param name="similarity_threshold" argument="-spectra:blackorwhitelist:similarity_threshold" type="float" optional="true" min="-1.0" max="1.0" value="-1.0" label="Similarity threshold when matching MS2 spectra" help="(-1 = disabled)"/>
513 <option value="Blackbody infrared radiative dissociation">Blackbody infrared radiative dissociation</option> 237 <param name="rt" argument="-spectra:blackorwhitelist:rt" type="float" optional="true" value="0.01" label="Retention tolerance [s] when matching precursor positions" help="(-1 = disabled)"/>
514 <option value="Electron capture dissociation">Electron capture dissociation</option> 238 <param name="mz" argument="-spectra:blackorwhitelist:mz" type="float" optional="true" value="0.01" label="m/z tolerance [Th] when matching precursor positions" help="(-1 = disabled)"/>
515 <option value="Infrared multiphoton dissociation">Infrared multiphoton dissociation</option> 239 <param name="use_ppm_tolerance" argument="-spectra:blackorwhitelist:use_ppm_tolerance" type="text" optional="true" value="false" label="If ppm tolerance should be used" help="Otherwise Da are used">
516 <option value="Sustained off-resonance irradiation">Sustained off-resonance irradiation</option> 240 <expand macro="list_string_san"/>
517 <option value="High-energy collision-induced dissociation">High-energy collision-induced dissociation</option> 241 </param>
518 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> 242 <param name="blacklist" argument="-spectra:blackorwhitelist:blacklist" type="boolean" truevalue="true" falsevalue="false" checked="true" label="True: remove matched MS2" help="False: retain matched MS2 spectra. Other levels are kept"/>
519 <option value="Photodissociation">Photodissociation</option> 243 </section>
520 <option value="Electron transfer dissociation">Electron transfer dissociation</option> 244 </section>
521 <option value="Pulsed q dissociation">Pulsed q dissociation</option> 245 <section name="feature" title="Feature data options" help="" expanded="false">
522 </param> 246 <param name="q" argument="-feature:q" type="text" optional="true" value=":" label="Overall quality range to extract [0:1]" help="">
523 <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) "> 247 <expand macro="list_string_san"/>
524 <sanitizer> 248 </param>
525 <valid initial="string.printable"> 249 </section>
526 <remove value="'"/> 250 <section name="consensus" title="Consensus feature data options" help="" expanded="false">
527 <remove value="&quot;"/> 251 <param name="map" argument="-consensus:map" type="text" optional="true" value="" label="Non-empty list of maps to be extracted from a consensus (indices are 0-based)" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
528 </valid> 252 <expand macro="list_integer_valsan"/>
529 </sanitizer> 253 </param>
530 </param> 254 <param name="map_and" argument="-consensus:map_and" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Consensus features are kept only if they contain exactly one feature from each map (as given above in 'map')" help=""/>
531 <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) "> 255 <section name="blackorwhitelist" title="Black or white listing of of MS2 spectra by consensus features" help="" expanded="false">
532 <sanitizer> 256 <param name="blacklist" argument="-consensus:blackorwhitelist:blacklist" type="boolean" truevalue="true" falsevalue="false" checked="true" label="True: remove matched MS2" help="False: retain matched MS2 spectra. Other levels are kept"/>
533 <valid initial="string.printable"> 257 <param name="file" argument="-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" help="Matching tolerances are taken from 'consensus:blackorwhitelist:rt' and 'consensus:blackorwhitelist:mz' options.. If consensus:blackorwhitelist:maps is specified, only these will be used.. select consensusxml data sets(s)"/>
534 <remove value="'"/> 258 <param name="maps" argument="-consensus:blackorwhitelist:maps" type="text" optional="true" value="" label="Maps used for black/white list filtering" help=" (space separated list, in order to allow for spaces in list items surround them by single quotes)">
535 <remove value="&quot;"/> 259 <expand macro="list_integer_valsan"/>
536 </valid> 260 </param>
537 </sanitizer> 261 <param name="rt" argument="-consensus:blackorwhitelist:rt" type="float" optional="true" min="0.0" value="60.0" label="Retention tolerance [s] for precursor to consensus feature position" help=""/>
538 </param> 262 <param name="mz" argument="-consensus:blackorwhitelist:mz" type="float" optional="true" min="0.0" value="0.01" label="m/z tolerance [Th] for precursor to consensus feature position" help=""/>
539 <param name="param_spectra_select_polarity" display="radio" type="select" optional="True" label="Retain MSn scans with a certain scan polarity" help="(-select_polarity) "> 263 <param name="use_ppm_tolerance" argument="-consensus:blackorwhitelist:use_ppm_tolerance" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If ppm tolerance should be used" help="Otherwise Da are used"/>
540 <option value="unknown">unknown</option> 264 </section>
541 <option value="positive">positive</option> 265 </section>
542 <option value="negative">negative</option> 266 <section name="f_and_c" title="Feature &amp; Consensus data options" help="" expanded="false">
543 </param> 267 <param name="charge" argument="-f_and_c:charge" type="text" optional="true" value=":" label="Charge range to extract" help="">
544 <param name="param_feature_q" type="text" size="30" value=":" label="Overall quality range to extract [0:1]" help="(-q) "> 268 <expand macro="list_string_san"/>
545 <sanitizer> 269 </param>
546 <valid initial="string.printable"> 270 <param name="size" argument="-f_and_c:size" type="text" optional="true" value=":" label="Size range to extract" help="">
547 <remove value="'"/> 271 <expand macro="list_string_san"/>
548 <remove value="&quot;"/> 272 </param>
549 </valid> 273 <param name="remove_meta" argument="-f_and_c:remove_meta" type="text" optional="true" value="" label="Expects a 3-tuple (=3 entries in the list)" help="i.e. &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!)! (space separated list, in order to allow for spaces in list items surround them by single quotes)">
550 </sanitizer> 274 <expand macro="list_string_val"/>
551 </param> 275 <expand macro="list_string_san"/>
552 <repeat name="rep_param_consensus_map" min="0" title="param_consensus_map"> 276 </param>
553 <param name="param_consensus_map" type="text" size="30" value="0" label="Maps to be extracted from a consensus" help="(-map) "> 277 </section>
554 <sanitizer> 278 <section name="id" title="ID options" help="The Priority of the id-flags is: remove_annotated_features / remove_unannotated_features -&gt; remove_clashes -&gt; keep_best_score_id -&gt; sequences_whitelist / accessions_whitelist" expanded="false">
555 <valid initial="string.printable"> 279 <param name="remove_clashes" argument="-id:remove_clashes" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features with id clashes (different sequences mapped to one feature)" help=""/>
556 <remove value="'"/> 280 <param name="keep_best_score_id" argument="-id:keep_best_score_id" type="boolean" truevalue="true" falsevalue="false" checked="false" label="in case of multiple peptide identifications, keep only the id with best score" help=""/>
557 <remove value="&quot;"/> 281 <param name="sequences_whitelist" argument="-id:sequences_whitelist" type="text" optional="true" value="" label="Keep only features containing whitelisted substrings" help="e.g. features containing LYSNLVER or the modification (Oxidation). To control comparison method used for whitelisting, see 'id:sequence_comparison_method' (space separated list, in order to allow for spaces in list items surround them by single quotes)">
558 </valid> 282 <expand macro="list_string_val"/>
559 </sanitizer> 283 <expand macro="list_string_san"/>
560 </param> 284 </param>
561 </repeat> 285 <param name="sequence_comparison_method" argument="-id:sequence_comparison_method" display="radio" type="select" optional="false" label="Comparison method used to determine if a feature is whitelisted" help="">
562 <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) "/> 286 <option value="substring" selected="true">substring</option>
563 <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"> 287 <option value="exact">exact</option>
564 <option value="false">false</option> 288 <expand macro="list_string_san"/>
565 <option value="true" selected="true">true</option> 289 </param>
566 </param> 290 <param name="accessions_whitelist" argument="-id:accessions_whitelist" type="text" optional="true" value="" label="keep only features with white listed accessions" help="e.g. sp|P02662|CASA1_BOVIN (space separated list, in order to allow for spaces in list items surround them by single quotes)">
567 <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;"/> 291 <expand macro="list_string_val"/>
568 <repeat name="rep_param_consensus_blackorwhitelist_maps" min="0" title="param_consensus_blackorwhitelist_maps"> 292 <expand macro="list_string_san"/>
569 <param name="param_consensus_blackorwhitelist_maps" type="text" size="30" value="0" label="Maps used for black/white list filtering" help="(-maps) "> 293 </param>
570 <sanitizer> 294 <param name="remove_annotated_features" argument="-id:remove_annotated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features with annotations" help=""/>
571 <valid initial="string.printable"> 295 <param name="remove_unannotated_features" argument="-id:remove_unannotated_features" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove features without annotations" help=""/>
572 <remove value="'"/> 296 <param name="remove_unassigned_ids" argument="-id:remove_unassigned_ids" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Remove unassigned peptide identifications" help=""/>
573 <remove value="&quot;"/> 297 <param name="blacklist" argument="-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" help="Matching tolerances are taken from 'id:rt' and 'id:mz' options.. 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 select idxml data sets(s)"/>
574 </valid> 298 <param name="rt" argument="-id:rt" type="float" optional="true" min="0.0" value="0.1" label="Retention tolerance [s] for precursor to id position" help=""/>
575 </sanitizer> 299 <param name="mz" argument="-id:mz" type="float" optional="true" min="0.0" value="0.001" label="m/z tolerance [Th] for precursor to id position" help=""/>
576 </param> 300 <param name="blacklist_imperfect" argument="-id:blacklist_imperfect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Allow for mismatching precursor positions (see 'id:blacklist')" help=""/>
577 </repeat> 301 </section>
578 <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) "/> 302 <section name="algorithm" title="S/N algorithm section" help="" expanded="false">
579 <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) "/> 303 <section name="SignalToNoise" title="" help="" expanded="false">
580 <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"/> 304 <param name="max_intensity" argument="-algorithm:SignalToNoise:max_intensity" type="integer" optional="true" min="-1" value="-1" label="maximal intensity considered for histogram construction" help="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"/>
581 <param name="param_f_and_c_charge" type="text" size="30" value=":" label="Charge range to extract" help="(-charge) "> 305 <param name="auto_max_stdev_factor" argument="-algorithm:SignalToNoise:auto_max_stdev_factor" type="float" optional="true" min="0.0" max="999.0" value="3.0" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 0): mean + 'auto_max_stdev_factor' * stdev" help=""/>
582 <sanitizer> 306 <param name="auto_max_percentile" argument="-algorithm:SignalToNoise:auto_max_percentile" type="integer" optional="true" min="0" max="100" value="95" label="parameter for 'max_intensity' estimation (if 'auto_mode' == 1): auto_max_percentile th percentile" help=""/>
583 <valid initial="string.printable"> 307 <param name="auto_mode" argument="-algorithm:SignalToNoise:auto_mode" type="integer" optional="true" min="-1" max="1" 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=""/>
584 <remove value="'"/> 308 <param name="win_len" argument="-algorithm:SignalToNoise:win_len" type="float" optional="true" min="1.0" value="200.0" label="window length in Thomson" help=""/>
585 <remove value="&quot;"/> 309 <param name="bin_count" argument="-algorithm:SignalToNoise:bin_count" type="integer" optional="true" min="3" value="30" label="number of bins for intensity values" help=""/>
586 </valid> 310 <param name="min_required_elements" argument="-algorithm:SignalToNoise: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=""/>
587 </sanitizer> 311 <param name="noise_for_empty_window" argument="-algorithm:SignalToNoise:noise_for_empty_window" type="float" optional="true" value="1e+20" label="noise value used for sparse windows" help=""/>
588 </param> 312 <param name="write_log_messages" argument="-algorithm:SignalToNoise:write_log_messages" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Write out log messages in case of sparse windows or median in rightmost histogram bin" help=""/>
589 <param name="param_f_and_c_size" type="text" size="30" value=":" label="Size range to extract" help="(-size) "> 313 </section>
590 <sanitizer> 314 </section>
591 <valid initial="string.printable"> 315 <expand macro="adv_opts_macro">
592 <remove value="'"/> 316 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
593 <remove value="&quot;"/> 317 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
594 </valid> 318 <expand macro="list_string_san"/>
595 </sanitizer> 319 </param>
596 </param>
597 <repeat name="rep_param_f_and_c_remove_meta" min="0" title="param_f_and_c_remove_meta">
598 <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!)!">
599 <sanitizer>
600 <valid initial="string.printable">
601 <remove value="'"/>
602 <remove value="&quot;"/>
603 </valid>
604 </sanitizer>
605 </param>
606 </repeat>
607 <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) "/>
608 <repeat name="rep_param_id_sequences_whitelist" min="0" title="param_id_sequences_whitelist">
609 <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)">
610 <sanitizer>
611 <valid initial="string.printable">
612 <remove value="'"/>
613 <remove value="&quot;"/>
614 </valid>
615 </sanitizer>
616 </param>
617 </repeat>
618 <repeat name="rep_param_id_accessions_whitelist" min="0" title="param_id_accessions_whitelist">
619 <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">
620 <sanitizer>
621 <valid initial="string.printable">
622 <remove value="'"/>
623 <remove value="&quot;"/>
624 </valid>
625 </sanitizer>
626 </param>
627 </repeat>
628 <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) "/>
629 <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) "/>
630 <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) "/>
631 <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"/>
632 <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) "/>
633 <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) "/>
634 <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) "/>
635 <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) "/>
636 <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) "/>
637 <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) "/>
638 <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) ">
639 <option value="true" selected="true">true</option>
640 <option value="false">false</option>
641 </param>
642 <expand macro="advanced_options">
643 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
644 <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) "/>
645 <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"/>
646 <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) "/>
647 <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) "/>
648 <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) "/>
649 <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) "/>
650 </expand> 320 </expand>
321 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
322 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
323 </param>
651 </inputs> 324 </inputs>
652 <outputs> 325 <outputs>
653 <data name="param_out" metadata_source="param_in" format="input"/> 326 <data name="out" label="${tool.name} on ${on_string}: out">
327 <change_format>
328 <when input="out_type" value="consensusXML" format="consensusxml"/>
329 <when input="out_type" value="featureXML" format="featurexml"/>
330 <when input="out_type" value="mzML" format="mzml"/>
331 </change_format>
332 </data>
333 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
334 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
335 </data>
654 </outputs> 336 </outputs>
655 <help>Extracts or manipulates portions of data from peak, feature or consensus-feature files. 337 <tests>
656 338 <expand macro="autotest_FileFilter"/>
657 339 <expand macro="manutest_FileFilter"/>
658 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileFilter.html</help> 340 </tests>
341 <help><![CDATA[Extracts or manipulates portions of data from peak, feature or consensus-feature files.
342
343
344 For more information, visit http://www.openms.de/documentation/TOPP_FileFilter.html]]></help>
345 <expand macro="references"/>
659 </tool> 346 </tool>