Mercurial > repos > galaxyp > fragpipe

comparison msfragger_macros.xml @ 7:b4f6df8fa89b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/fragpipe commit 9d8b2338a6a513124bc58223637ee4c5813e0bb4
author galaxyp
date Wed, 01 Oct 2025 22:20:54 +0000
parents 59fec1e2a6c3
children
comparison
equal deleted inserted replaced
6:59fec1e2a6c3 7:b4f6df8fa89b
36 36
37 <!-- The following xml elements define the parameters for each given workflow --> 37 <!-- The following xml elements define the parameters for each given workflow -->
38 <xml name="msfragger_default"> 38 <xml name="msfragger_default">
39 <expand macro="search_tolerances"/> 39 <expand macro="search_tolerances"/>
40 <expand macro="digestion"/> 40 <expand macro="digestion"/>
41 <expand macro="variable_modification"/> 41 <expand macro="variable_modification" mod_3="true"/>
42 <expand macro="static_modification"/> 42 <expand macro="static_modification"/>
43 <expand macro="glyco_labile"/> 43 <expand macro="glyco_labile"/>
44 <expand macro="mass_offsets"/> 44 <expand macro="mass_offsets"/>
45 <expand macro="spectrum_processing"/> 45 <expand macro="spectrum_processing"/>
46 <expand macro="open_search_options"/> 46 <expand macro="open_search_options"/>
48 <expand macro="advanced_options"/> 48 <expand macro="advanced_options"/>
49 </xml> 49 </xml>
50 <xml name="msfragger_open"> 50 <xml name="msfragger_open">
51 <expand macro="search_tolerances"/> 51 <expand macro="search_tolerances"/>
52 <expand macro="digestion"/> 52 <expand macro="digestion"/>
53 <expand macro="variable_modification"/> 53 <expand macro="variable_modification" mod_3="true"/>
54 <expand macro="static_modification"/> 54 <expand macro="static_modification"/>
55 <expand macro="glyco_labile"/> 55 <expand macro="glyco_labile"/>
56 <expand macro="mass_offsets"/> 56 <expand macro="mass_offsets"/>
57 <expand macro="spectrum_processing" mode_selected="false" mode_corrected="true"/> 57 <expand macro="spectrum_processing" mode_selected="false" mode_corrected="true"/>
58 <expand macro="open_search_options" localize="true"/> 58 <expand macro="open_search_options" localize="true"/>
60 <expand macro="advanced_options"/> 60 <expand macro="advanced_options"/>
61 </xml> 61 </xml>
62 <xml name="msfragger_nonspecific_HLA"> 62 <xml name="msfragger_nonspecific_HLA">
63 <expand macro="search_tolerances" precursor_mass_lower="-20" precursor_mass_upper="20"/> 63 <expand macro="search_tolerances" precursor_mass_lower="-20" precursor_mass_upper="20"/>
64 <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false" digest_mass_range_min="200.0"/> 64 <expand macro="digestion" stricttrypsin="false" nonspecific="true" digest_max_length="25" termini_0="true" termini_2="false" digest_mass_range_min="200.0"/>
65 <expand macro="variable_modification"/> 65 <expand macro="variable_modification" mod_2="true" mod_group_hla="true"/>
66 <expand macro="static_modification"/> 66 <expand macro="static_modification" check_cysteine="false"/>
67 <expand macro="glyco_labile"/> 67 <expand macro="glyco_labile"/>
68 <expand macro="mass_offsets"/> 68 <expand macro="mass_offsets"/>
69 <expand macro="spectrum_processing" transform_none="false" transform_sqrt="true"/> 69 <expand macro="spectrum_processing" transform_none="false" transform_sqrt="true"/>
70 <expand macro="open_search_options"/> 70 <expand macro="open_search_options"/>
71 <expand macro="modeling_output"/> 71 <expand macro="modeling_output"/>
72 <expand macro="advanced_options"/> 72 <expand macro="advanced_options"/>
73 </xml> 73 </xml>
74 <xml name="msfragger_LFQ_MBR"> 74 <xml name="msfragger_LFQ_MBR">
75 <expand macro="search_tolerances"/> 75 <expand macro="search_tolerances"/>
76 <expand macro="digestion"/> 76 <expand macro="digestion"/>
77 <expand macro="variable_modification"/> 77 <expand macro="variable_modification" mod_3="true"/>
78 <expand macro="static_modification"/> 78 <expand macro="static_modification"/>
79 <expand macro="glyco_labile"/> 79 <expand macro="glyco_labile"/>
80 <expand macro="mass_offsets"/> 80 <expand macro="mass_offsets"/>
81 <expand macro="spectrum_processing"/> 81 <expand macro="spectrum_processing"/>
82 <expand macro="open_search_options"/> 82 <expand macro="open_search_options"/>
84 <expand macro="advanced_options"/> 84 <expand macro="advanced_options"/>
85 </xml> 85 </xml>
86 <xml name="msfragger_TMT"> 86 <xml name="msfragger_TMT">
87 <expand macro="search_tolerances"/> 87 <expand macro="search_tolerances"/>
88 <expand macro="digestion" digest_mass_range_min="200.0"/> 88 <expand macro="digestion" digest_mass_range_min="200.0"/>
89 <expand macro="variable_modification"/> 89 <expand macro="variable_modification" mod_3="true" mod_group_tmt="true"/>
90 <expand macro="static_modification" lysine_value="229.16293"/>
91 <expand macro="glyco_labile"/>
92 <expand macro="mass_offsets"/>
93 <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/>
94 <expand macro="open_search_options"/>
95 <expand macro="modeling_output"/>
96 <expand macro="advanced_options"/>
97 </xml>
98 <xml name="msfragger_dia_speclib_quant">
99 <expand macro="search_tolerances"/>
100 <expand macro="digestion" allowed_missed_cleavage_1="1" allowed_missed_cleavage_2="1"/>
101 <expand macro="variable_modification" mod_1="true"/>
90 <expand macro="static_modification"/> 102 <expand macro="static_modification"/>
91 <expand macro="glyco_labile"/> 103 <expand macro="glyco_labile"/>
92 <expand macro="mass_offsets"/> 104 <expand macro="mass_offsets"/>
93 <expand macro="spectrum_processing" clear_mz_range_min="125.5" clear_mz_range_max="131.5"/> 105 <expand macro="spectrum_processing" check_spectral_files="false"/>
94 <expand macro="open_search_options"/> 106 <expand macro="open_search_options"/>
95 <expand macro="modeling_output"/> 107 <expand macro="modeling_output"/>
96 <expand macro="advanced_options"/> 108 <expand macro="advanced_options"/>
97 </xml> 109 </xml>
98 110
221 233
222 <xml name="cleavage" token_search_enzyme_name="trypsin" token_cut="KR" token_nocut="P"> 234 <xml name="cleavage" token_search_enzyme_name="trypsin" token_cut="KR" token_nocut="P">
223 <param name="search_enzyme_name" type="text" value="@SEARCH_ENZYME_NAME@" 235 <param name="search_enzyme_name" type="text" value="@SEARCH_ENZYME_NAME@"
224 label="Digestion Enzyme" help="Name of enzyme to be written to the pepXML file."/> 236 label="Digestion Enzyme" help="Name of enzyme to be written to the pepXML file."/>
225 <param name="search_enzyme_cut" type="text" value="@CUT@" 237 <param name="search_enzyme_cut" type="text" value="@CUT@"
226 label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts Default: KR"/> 238 label="Residues after which the enzyme cuts" help="search_enzyme_cutafter Residues after which the enzyme cuts"/>
227 <param name="search_enzyme_nocut" type="text" value="@NOCUT@" 239 <param name="search_enzyme_nocut" type="text" value="@NOCUT@"
228 label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore) Default: P"/> 240 label="Residues that the enzyme will not cut before" help="search_enzyme_butnotafter - (misnomer: should really be called butnotbefore)"/>
229 </xml> 241 </xml>
230 <!-- wagnerr here in final param review --> 242 <xml name="digest" token_stricttrypsin="true" token_nonspecific="false" token_allowed_missed_cleavage="2">
231 <xml name="digest" token_stricttrypsin="true" token_nonspecific="false">
232 <conditional name="digest"> 243 <conditional name="digest">
233 <param name="search_enzyme" type="select" label="Protein Digestion Enzyme"> 244 <param name="search_enzyme" type="select" label="Protein Digestion Enzyme">
234 <option value="trypsin">trypsin</option> 245 <option value="trypsin">trypsin</option>
235 <option value="stricttrypsin" selected="@STRICTTRYPSIN@">stricttrypsin</option> 246 <option value="stricttrypsin" selected="@STRICTTRYPSIN@">stricttrypsin</option>
236 <option value="argc">argc</option> 247 <option value="argc">argc</option>
282 </when> 293 </when>
283 <when value="lysc-p"> 294 <when value="lysc-p">
284 <expand macro="cleavage" search_enzyme_name="lysc-p" cut="K" nocut=""/> 295 <expand macro="cleavage" search_enzyme_name="lysc-p" cut="K" nocut=""/>
285 </when> 296 </when>
286 <when value="nonspecific"> 297 <when value="nonspecific">
287 <expand macro="cleavage" search_enzyme_name="nonspecific" cut="-" nocut=""/> 298 <expand macro="cleavage" search_enzyme_name="nonspecific" cut="@" nocut=""/>
288 </when> 299 </when>
289 <when value="custom"> 300 <when value="custom">
290 <expand macro="cleavage" search_enzyme_name="custom" cut="" nocut=""/> 301 <expand macro="cleavage" search_enzyme_name="custom" cut="" nocut=""/>
291 </when> 302 </when>
292 <when value="trypsin/chymotrypsin"> 303 <when value="trypsin/chymotrypsin">
303 </when> 314 </when>
304 <when value="trypsin_r"> 315 <when value="trypsin_r">
305 <expand macro="cleavage" search_enzyme_name="trypsin_r" cut="R" nocut="P"/> 316 <expand macro="cleavage" search_enzyme_name="trypsin_r" cut="R" nocut="P"/>
306 </when> 317 </when>
307 </conditional> 318 </conditional>
308 <param name="allowed_missed_cleavage" type="integer" value="2" min="0" max="5" optional="true" 319 <param name="allowed_missed_cleavage" type="integer" value="@ALLOWED_MISSED_CLEAVAGE@" min="0" max="5" optional="true"
309 label="Allowed number of missed cleavages"/> 320 label="Allowed number of missed cleavages"/>
310 <param name="search_enzyme_sense" type="select" label="Protein Digestion Enzyme"> 321 <param name="search_enzyme_sense" type="select" label="Search Enzyme Sense">
311 <option value="C">C</option> 322 <option value="C">C</option>
312 <option value="N">N</option> 323 <option value="N">N</option>
313 </param> 324 </param>
314 </xml> 325 </xml>
315 326
316 <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0"> 327 <xml name="digestion" token_stricttrypsin="true" token_nonspecific="false" token_digest_max_length="50" token_termini_0="false" token_termini_1="false" token_termini_2="true" token_digest_mass_range_min="500.0" token_digest_mass_range_max="5000.0" token_allowed_missed_cleavage_1="2" token_allowed_missed_cleavage_2="2">
317 <section name="digestion" expanded="false" title="In-silico Digestion Parameters"> 328 <section name="digestion" expanded="false" title="In-silico Digestion Parameters">
318 <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@"/> 329 <expand macro="digest" stricttrypsin="@STRICTTRYPSIN@" nonspecific="@NONSPECIFIC@" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_1@"/>
319 <conditional name="enzyme2"> 330 <conditional name="enzyme2">
320 <param name="digest2" type="select" label="Second Enzyme Digest"> 331 <param name="digest2" type="select" label="Second Enzyme Digest">
321 <option value="no">No</option> 332 <option value="no">No</option>
322 <option value="yes">Yes</option> 333 <option value="yes">Yes</option>
323 </param> 334 </param>
324 <when value="no"/> 335 <when value="no"/>
325 <when value="yes"> 336 <when value="yes">
326 <expand macro="digest" stricttrypsin="false" nonspecific="false"/> 337 <expand macro="digest" stricttrypsin="false" nonspecific="false" allowed_missed_cleavage="@ALLOWED_MISSED_CLEAVAGE_2@"/>
327 </when> 338 </when>
328 </conditional> 339 </conditional>
329 <param name="num_enzyme_termini" type="select" label="Number of enzyme termini"> 340 <param name="num_enzyme_termini" type="select" label="Number of enzyme termini">
330 <option value="0" selected="@TERMINI_0@">0 - non-enzymatic</option> 341 <option value="0" selected="@TERMINI_0@">0 - non-enzymatic</option>
331 <option value="1" selected="@TERMINI_1@">1 - semi-enzymatic</option> 342 <option value="1" selected="@TERMINI_1@">1 - semi-enzymatic</option>
344 <token name="@DIGESTION@"><![CDATA[ 355 <token name="@DIGESTION@"><![CDATA[
345 ## digest parameters 356 ## digest parameters
346 ##enzyme_1 357 ##enzyme_1
347 #set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name 358 #set $msfragger_dict['search_enzyme_name_1'] = $prefix.digestion.digest.search_enzyme_name
348 #set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name 359 #set $msfragger_dict['misc.fragger.enzyme-dropdown-1'] = $prefix.digestion.digest.search_enzyme_name
349 #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut 360 #if $prefix.digestion.search_enzyme_cut == '__at__'
361 #set $msfragger_dict['search_enzyme_cut_1'] = '@'
362 #else
363 #set $msfragger_dict['search_enzyme_cut_1'] = $prefix.digestion.digest.search_enzyme_cut
364 #end if
350 #set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut 365 #set $msfragger_dict['search_enzyme_nocut_1'] = $prefix.digestion.digest.search_enzyme_nocut
351 #if $prefix.digestion.allowed_missed_cleavage != '' 366 #if $prefix.digestion.allowed_missed_cleavage != ''
352 #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage 367 #set $msfragger_dict['allowed_missed_cleavage_1'] = $prefix.digestion.allowed_missed_cleavage
353 #end if 368 #end if
354 #if $prefix.digestion.search_enzyme_sense != 'None' 369 #if $prefix.digestion.search_enzyme_sense != 'None'
356 #end if 371 #end if
357 ##enzyme_2 372 ##enzyme_2
358 #if $prefix.digestion.enzyme2.digest2 == 'yes' 373 #if $prefix.digestion.enzyme2.digest2 == 'yes'
359 #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name 374 #set $msfragger_dict['search_enzyme_name_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name
360 #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name 375 #set $msfragger_dict['misc.fragger.enzyme-dropdown-2'] = $prefix.digestion.enzyme2.digest.search_enzyme_name
361 #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut 376 #if $prefix.digestion.enzyme2.digest.search_enzyme_cut == '__at__'
377 #set $msfragger_dict['search_enzyme_cut_2'] = '@'
378 #else
379 #set $msfragger_dict['search_enzyme_cut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_cut
380 #end if
362 #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut 381 #set $msfragger_dict['search_enzyme_nocut_2'] = $prefix.digestion.enzyme2.digest.search_enzyme_nocut
363 #if $prefix.digestion.enzyme2.allowed_missed_cleavage != '' 382 #if $prefix.digestion.enzyme2.allowed_missed_cleavage != ''
364 #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage 383 #set $msfragger_dict['allowed_missed_cleavage_2'] = $prefix.digestion.enzyme2.allowed_missed_cleavage
365 #end if 384 #end if
366 #if $prefix.digestion.enzyme2.search_enzyme_sense != 'None' 385 #if $prefix.digestion.enzyme2.search_enzyme_sense != 'None'
384 #if $prefix.digestion.digest_mass_range_min != '' 403 #if $prefix.digestion.digest_mass_range_min != ''
385 #set $msfragger_dict['misc.fragger.digest-mass-hi'] = $prefix.digestion.digest_mass_range_max 404 #set $msfragger_dict['misc.fragger.digest-mass-hi'] = $prefix.digestion.digest_mass_range_max
386 #end if 405 #end if
387 ]]></token> 406 ]]></token>
388 407
389 <xml name="variable_modifications">
390 <option value="15.99491461956 M 3">Oxidation of M (15.99491461956) modaa</option>
391 <option value="42.0105646837 &#91;^ 1">Acetylation of peptide N-term (42.0105646837) modn_peptide</option>
392 <option value="79.96633052074999 STY 3">Phosphorylation of STY (79.96633052074999) modaa</option>
393 <option value="229.16293213472 n^ 1">TMT 10-plex of peptide N-term (229.16293213472) modn_peptide</option>
394 <option value="229.169252 n^ 1">TMT 11-plex of peptide N-term (229.169252) modn_peptide</option>
395 <option value="229.16293213472 S 1">TMT 10-plex of S (229.16293213472) modaa</option>
396 <option value="229.169252 S 1">TMT 11-plex of S (229.169252) modaa</option>
397 <option value="-18.0105646837 nE 1">Pyrolidone from E (-18.0105646837) modnaa_peptide</option>
398 </xml>
399
400 <token name="@RE_FLOAT@">[+-]?\d+(\.\d*)?</token> 408 <token name="@RE_FLOAT@">[+-]?\d+(\.\d*)?</token>
401 <token name="@RE_AA@">([A-Z]+|(c[A-Z*])+|(n[\^A-Z*])+|\[\^|\])</token> 409 <token name="@RE_AA@">([A-Z]+|(c[A-Z*])+|(n[\^A-Z*])+|\[\^|\])</token>
402 <token name="@RE_MOD@">@RE_FLOAT@,@RE_AA@,\d</token> 410 <token name="@RE_MOD@">@RE_FLOAT@,@RE_AA@,\d</token>
403 <token name="@RE_MODS@">@RE_MOD@(;\s*@RE_MOD@)*</token> 411 <token name="@RE_MODS@">@RE_MOD@(;\s*@RE_MOD@)*</token>
404 <xml name="variable_modification" token_max_variable_mods_per_peptide="3"> 412 <xml name="variable_modification" token_max_variable_mods_per_peptide="3" token_mod_1="false" token_mod_2="false" token_mod_3="false" token_mod_4="true" token_mod_group_hla="false" token_mod_group_tmt="false">
405 <section name="variable_modification" expanded="false" title="Variable Modifications"> 413 <section name="variable_modification" expanded="false" title="Variable Modifications">
406 <param name="max_variable_mods_per_peptide" type="integer" value="@MAX_VARIABLE_MODS_PER_PEPTIDE@" min="0" max="5" optional="true" 414 <param name="max_variable_mods_per_peptide" type="integer" value="@MAX_VARIABLE_MODS_PER_PEPTIDE@" min="0" max="5" optional="true"
407 label="Maximum total number of variable modifications per peptide"/> 415 label="Maximum total number of variable modifications per peptide"/>
408 <param name="variable_mods_select" type="select" optional="true" multiple="true" label="Select Variable Modifications"> 416 <param name="variable_mods_select" type="select" optional="true" multiple="true" label="Select Variable Modifications">
409 <expand macro="variable_modifications"/> 417 <option value="15.99491461956 M 1" selected="@MOD_1@">15.99491461956 M 1</option>
418 <option value="15.99491461956 M 2" selected="@MOD_2@">15.99491461956 M 2</option>
419 <option value="15.99491461956 M 3" selected="@MOD_3@">15.99491461956 M 3</option>
420 <option value="42.0105646837 ntermsite^ 1" selected="@MOD_4@">42.0105646837 [^ 1</option>
421 <option value="-17.0265 nQ 1" selected="@MOD_GROUP_HLA@">-17.0265 nQ 1</option>
422 <option value="-18.0106 nE 1" selected="@MOD_GROUP_HLA@">-18.0106 nE 1</option>
423 <option value="119.0041 C 1" selected="@MOD_GROUP_HLA@">119.0041 C 1</option>
424 <option value="79.96633052074999 STY 3">79.96633052074999 STY 3</option>
425 <option value="229.16293213472 n^ 1" selected="@MOD_GROUP_TMT@">229.16293213472 n^ 1</option>
426 <option value="229.16293213472 S 1" selected="@MOD_GROUP_TMT@">229.16293213472 S 1</option>
427 <option value="-18.0105646837 nE 1">-18.0105646837 nE 1</option>
410 </param> 428 </param>
411 <param name="variable_mods" type="text" area="True" size="120x7" value="" optional="true" 429 <param name="variable_mods" type="text" area="True" size="120x7" value="" optional="true"
412 label="Enter Variable Modifications"> 430 label="Enter Variable Modifications">
413 <help><![CDATA[ 431 <help><![CDATA[
414 Separate variable modifications with semicolons. Each modification has mass_change, residues, and max occurances values separated by commas. 432 Separate variable modifications with semicolons. Each modification has mass_change, residues, and max occurances values separated by commas.
434 </param> 452 </param>
435 <param name="clip_nTerm_M" type="select" optional="true" label="Trim protein N-terminal methionine as a variable modification"> 453 <param name="clip_nTerm_M" type="select" optional="true" label="Trim protein N-terminal methionine as a variable modification">
436 <option value="true">Yes</option> 454 <option value="true">Yes</option>
437 <option value="false">No</option> 455 <option value="false">No</option>
438 </param> 456 </param>
439 <param name="allow_multiple_variable_mods_on_residue" type="select" optional="true" label="Allow each amino acid to be modified by multiple variable modifications">
440 <option value="true">Yes</option>
441 <option value="false">No</option>
442 </param>
443 457
444 <param name="max_variable_mods_combinations" type="integer" value="5000" min="0" max="65534" optional="true" 458 <param name="max_variable_mods_combinations" type="integer" value="5000" min="0" max="65534" optional="true"
445 label="Maximum allowed number of modified variably modified peptides from each peptide sequence" 459 label="Maximum allowed number of modified variably modified peptides from each peptide sequence"
446 help="If a greater number than the maximum is generated, only the unmodified peptide is considered."/> 460 help="If a greater number than the maximum is generated, only the unmodified peptide is considered."/>
447 </section> 461 </section>
462 #set $msfragger_dict['use_all_mods_in_first_search'] = $prefix.variable_modification.use_all_mods_in_first_search 476 #set $msfragger_dict['use_all_mods_in_first_search'] = $prefix.variable_modification.use_all_mods_in_first_search
463 #end if 477 #end if
464 #if $prefix.variable_modification.clip_nTerm_M != 'None' 478 #if $prefix.variable_modification.clip_nTerm_M != 'None'
465 #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M 479 #set $msfragger_dict['clip_nTerm_M'] = $prefix.variable_modification.clip_nTerm_M
466 #end if 480 #end if
467 #if $prefix.variable_modification.allow_multiple_variable_mods_on_residue != 'None'
468 #set $msfragger_dict['allow_multiple_variable_mods_on_residue'] = $prefix.variable_modification.allow_multiple_variable_mods_on_residue
469 #end if
470 #if $prefix.variable_modification.max_variable_mods_combinations != "None" 481 #if $prefix.variable_modification.max_variable_mods_combinations != "None"
471 #set $msfragger_dict['max_variable_mods_combinations'] = $prefix.variable_modification.max_variable_mods_combinations 482 #set $msfragger_dict['max_variable_mods_combinations'] = $prefix.variable_modification.max_variable_mods_combinations
472 #end if 483 #end if
473 #set $vmods = [] 484 #set $vmods = []
474 #if $prefix.variable_modification.variable_mods_select != 'None' 485 #if $prefix.variable_modification.variable_mods_select != 'None'
475 #set $vmods = [x.replace(' ',',') for x in str($prefix.variable_modification.variable_mods_select).split(',')] 486 #set $vmods = [x.replace(' ',',').replace('ntermsite','[') for x in str($prefix.variable_modification.variable_mods_select).split(',')]
476 #end if 487 #end if
477 #if $prefix.variable_modification.variable_mods != '' 488 #if $prefix.variable_modification.variable_mods != ''
478 #set $vmods += [x.strip() for x in str($prefix.variable_modification.variable_mods).split(';')] 489 #set $vmods += [x.strip() for x in str($prefix.variable_modification.variable_mods).split(';')]
479 #end if 490 #end if
480 ]]></token> 491 ]]></token>
481 492
482 <xml name="static_modification"> 493 <xml name="static_modification" token_check_cysteine="true" token_lysine_value="0.0">
483 <section name="static_modification" expanded="false" title="Static Modifications"> 494 <section name="static_modification" expanded="false" title="Static Modifications">
484 <param name="add_Cterm_peptide" type="float" value="" optional="true" 495 <param name="add_Cterm_peptide_bool" type="boolean" checked="true"
485 label="Statically add mass in Da to C-terminal of peptide Default: 0.0" /> 496 label="Statically add mass in Da to C-terminal of peptide"/>
486 <param name="add_Nterm_peptide" type="float" value="" optional="true" 497 <param name="add_Cterm_peptide" type="float" value="0.0"
487 label="Statically add mass in Da to N-terminal of peptide Default: 0.0" /> 498 label="Statically add mass in Da to C-terminal of peptide" />
488 <param name="add_Cterm_protein" type="float" value="" optional="true" 499
489 label="Statically add mass in Da to C-terminal of protein Default: 0.0" /> 500 <param name="add_Nterm_peptide_bool" type="boolean" checked="true"
490 <param name="add_Nterm_protein" type="float" value="" optional="true" 501 label="Statically add mass in Da to N-terminal of peptide"/>
491 label="Statically add mass in Da to N-terminal of protein Default: 0.0" /> 502 <param name="add_Nterm_peptide" type="float" value="0.0"
492 <param name="add_A_alanine" type="float" value="" optional="true" 503 label="Statically add mass in Da to N-terminal of peptide" />
493 label="Statically add mass in Da to A (alanine) Default: 0.0" /> 504
494 <param name="add_R_arginine" type="float" value="" optional="true" 505 <param name="add_Cterm_protein_bool" type="boolean" checked="true"
495 label="Statically add mass in Da to R (arginine) Default: 0.0" /> 506 label="Statically add mass in Da to C-terminal of protein"/>
496 <param name="add_N_asparagine" type="float" value="" optional="true" 507 <param name="add_Cterm_protein" type="float" value="0.0"
497 label="Statically add mass in Da to N (asparagine) Default: 0.0" /> 508 label="Statically add mass in Da to C-terminal of protein" />
498 <param name="add_D_aspartic_acid" type="float" value="" optional="true" 509
499 label="Statically add mass in Da to D (aspartic_acid) Default: 0.0" /> 510 <param name="add_Nterm_protein_bool" type="boolean" checked="true"
500 <param name="add_C_cysteine" type="float" value="" optional="true" 511 label="Statically add mass in Da to N-terminal of protein"/>
501 label="Statically add mass in Da to C (cysteine) Default: 0.0" /> 512 <param name="add_Nterm_protein" type="float" value="0.0"
502 <param name="add_E_glutamic_acid" type="float" value="" optional="true" 513 label="Statically add mass in Da to N-terminal of protein" />
503 label="Statically add mass in Da to E (glutamic_acid) Default: 0.0" /> 514
504 <param name="add_Q_glutamine" type="float" value="" optional="true" 515 <param name="add_A_alanine_bool" type="boolean" checked="true"
505 label="Statically add mass in Da to Q (glutamine) Default: 0.0" /> 516 label="Statically add mass in Da to A (alanine)"/>
506 <param name="add_G_glycine" type="float" value="" optional="true" 517 <param name="add_A_alanine" type="float" value="0.0"
507 label="Statically add mass in Da to G (glycine) Default: 0.0" /> 518 label="Statically add mass in Da to A (alanine)" />
508 <param name="add_H_histidine" type="float" value="" optional="true" 519
509 label="Statically add mass in Da to H (histidine) Default: 0.0" /> 520 <param name="add_R_arginine_bool" type="boolean" checked="true"
510 <param name="add_I_isoleucine" type="float" value="" optional="true" 521 label="Statically add mass in Da to R (arginine)"/>
511 label="Statically add mass in Da to I (isoleucine) Default: 0.0" /> 522 <param name="add_R_arginine" type="float" value="0.0"
512 <param name="add_L_leucine" type="float" value="" optional="true" 523 label="Statically add mass in Da to R (arginine)" />
513 label="Statically add mass in Da to L (leucine) Default: 0.0" /> 524
514 <param name="add_K_lysine" type="float" value="" optional="true" 525 <param name="add_N_asparagine_bool" type="boolean" checked="true"
515 label="Statically add mass in Da to K (lysine) Default: 0.0" /> 526 label="Statically add mass in Da to N (asparagine)"/>
516 <param name="add_M_methionine" type="float" value="" optional="true" 527 <param name="add_N_asparagine" type="float" value="0.0"
517 label="Statically add mass in Da to M (methionine) Default: 0.0" /> 528 label="Statically add mass in Da to N (asparagine)" />
518 <param name="add_F_phenylalanine" type="float" value="" optional="true" 529
519 label="Statically add mass in Da to F (phenylalanine) Default: 0.0" /> 530 <param name="add_D_aspartic_acid_bool" type="boolean" checked="true"
520 <param name="add_P_proline" type="float" value="" optional="true" 531 label="Statically add mass in Da to D (aspartic_acid)"/>
521 label="Statically add mass in Da to P (proline) Default: 0.0" /> 532 <param name="add_D_aspartic_acid" type="float" value="0.0"
522 <param name="add_S_serine" type="float" value="" optional="true" 533 label="Statically add mass in Da to D (aspartic_acid)" />
523 label="Statically add mass in Da to S (serine) Default: 0.0" /> 534
524 <param name="add_T_threonine" type="float" value="" optional="true" 535 <param name="add_C_cysteine_bool" type="boolean" checked="@CHECK_CYSTEINE@"
525 label="Statically add mass in Da to T (threonine) Default: 0.0" /> 536 label="Statically add mass in Da to C (cysteine)"/>
526 <param name="add_W_tryptophan" type="float" value="" optional="true" 537 <param name="add_C_cysteine" type="float" value="57.02146"
527 label="Statically add mass in Da to W (tryptophan) Default: 0.0" /> 538 label="Statically add mass in Da to C (cysteine)" />
528 <param name="add_Y_tyrosine" type="float" value="" optional="true" 539
529 label="Statically add mass in Da to Y (tyrosine) Default: 0.0" /> 540 <param name="add_E_glutamic_acid_bool" type="boolean" checked="true"
530 <param name="add_V_valine" type="float" value="" optional="true" 541 label="Statically add mass in Da to E (glutamic_acid)"/>
531 label="Statically add mass in Da to V (valine) Default: 0.0" /> 542 <param name="add_E_glutamic_acid" type="float" value="0.0"
532 <param name="add_B_user_amino_acid" type="float" value="" optional="true" 543 label="Statically add mass in Da to E (glutamic_acid)" />
533 label="Statically add mass in Da to B (iuser_amino_acid) Default: 0.0" /> 544
534 <param name="add_J_user_amino_acid" type="float" value="" optional="true" 545 <param name="add_Q_glutamine_bool" type="boolean" checked="true"
535 label="Statically add mass in Da to J (iuser_amino_acid) Default: 0.0" /> 546 label="Statically add mass in Da to Q (glutamine)"/>
536 <param name="add_O_user_amino_acid" type="float" value="" optional="true" 547 <param name="add_Q_glutamine" type="float" value="0.0"
537 label="Statically add mass in Da to O (user_amino_acid) Default: 0.0" /> 548 label="Statically add mass in Da to Q (glutamine)" />
538 <param name="add_U_user_amino_acid" type="float" value="" optional="true" 549
539 label="Statically add mass in Da to U (iuser_amino_acid) Default: 0.0" /> 550 <param name="add_G_glycine_bool" type="boolean" checked="true"
540 <param name="add_X_user_amino_acid" type="float" value="" optional="true" 551 label="Statically add mass in Da to G (glycine)"/>
541 label="Statically add mass in Da to X (iuser_amino_acid) Default: 0.0" /> 552 <param name="add_G_glycine" type="float" value="0.0"
542 <param name="add_Z_user_amino_acid" type="float" value="" optional="true" 553 label="Statically add mass in Da to G (glycine)" />
543 label="Statically add mass in Da to Z (iuser_amino_acid) Default: 0.0" /> 554
555 <param name="add_H_histidine_bool" type="boolean" checked="true"
556 label="Statically add mass in Da to H (histidine)"/>
557 <param name="add_H_histidine" type="float" value="0.0"
558 label="Statically add mass in Da to H (histidine)" />
559
560 <param name="add_I_isoleucine_bool" type="boolean" checked="true"
561 label="Statically add mass in Da to I (isoleucine)"/>
562 <param name="add_I_isoleucine" type="float" value="0.0"
563 label="Statically add mass in Da to I (isoleucine)" />
564
565 <param name="add_L_leucine_bool" type="boolean" checked="true"
566 label="Statically add mass in Da to L (leucine)"/>
567 <param name="add_L_leucine" type="float" value="0.0"
568 label="Statically add mass in Da to L (leucine)" />
569
570 <param name="add_K_lysine_bool" type="boolean" checked="true"
571 label="Statically add mass in Da to K (lysine)"/>
572 <param name="add_K_lysine" type="float" value="@LYSINE_VALUE@"
573 label="Statically add mass in Da to K (lysine)" />
574
575 <param name="add_M_methionine_bool" type="boolean" checked="true"
576 label="Statically add mass in Da to M (methionine)"/>
577 <param name="add_M_methionine" type="float" value="0.0"
578 label="Statically add mass in Da to M (methionine)" />
579
580 <param name="add_F_phenylalanine_bool" type="boolean" checked="true"
581 label="Statically add mass in Da to F (phenylalanine)"/>
582 <param name="add_F_phenylalanine" type="float" value="0.0"
583 label="Statically add mass in Da to F (phenylalanine)" />
584
585 <param name="add_P_proline_bool" type="boolean" checked="true"
586 label="Statically add mass in Da to P (proline)"/>
587 <param name="add_P_proline" type="float" value="0.0"
588 label="Statically add mass in Da to P (proline)" />
589
590 <param name="add_S_serine_bool" type="boolean" checked="true"
591 label="Statically add mass in Da to S (serine)"/>
592 <param name="add_S_serine" type="float" value="0.0"
593 label="Statically add mass in Da to S (serine)" />
594
595 <param name="add_T_threonine_bool" type="boolean" checked="true"
596 label="Statically add mass in Da to T (threonine)"/>
597 <param name="add_T_threonine" type="float" value="0.0"
598 label="Statically add mass in Da to T (threonine)" />
599
600 <param name="add_W_tryptophan_bool" type="boolean" checked="true"
601 label="Statically add mass in Da to W (tryptophan)"/>
602 <param name="add_W_tryptophan" type="float" value="0.0"
603 label="Statically add mass in Da to W (tryptophan)" />
604
605 <param name="add_Y_tyrosine_bool" type="boolean" checked="true"
606 label="Statically add mass in Da to Y (tyrosine)"/>
607 <param name="add_Y_tyrosine" type="float" value="0.0"
608 label="Statically add mass in Da to Y (tyrosine)" />
609
610 <param name="add_V_valine_bool" type="boolean" checked="true"
611 label="Statically add mass in Da to V (valine)"/>
612 <param name="add_V_valine" type="float" value="0.0"
613 label="Statically add mass in Da to V (valine)" />
614
615 <param name="add_B_user_amino_acid_bool" type="boolean" checked="true"
616 label="Statically add mass in Da to B (iuser_amino_acid)"/>
617 <param name="add_B_user_amino_acid" type="float" value="0.0"
618 label="Statically add mass in Da to B (iuser_amino_acid)" />
619
620 <param name="add_J_user_amino_acid_bool" type="boolean" checked="true"
621 label="Statically add mass in Da to J (iuser_amino_acid)"/>
622 <param name="add_J_user_amino_acid" type="float" value="0.0"
623 label="Statically add mass in Da to J (iuser_amino_acid)" />
624
625 <param name="add_O_user_amino_acid_bool" type="boolean" checked="true"
626 label="Statically add mass in Da to O (user_amino_acid)"/>
627 <param name="add_O_user_amino_acid" type="float" value="0.0"
628 label="Statically add mass in Da to O (user_amino_acid)" />
629
630 <param name="add_U_user_amino_acid_bool" type="boolean" checked="true"
631 label="Statically add mass in Da to U (iuser_amino_acid)"/>
632 <param name="add_U_user_amino_acid" type="float" value="0.0"
633 label="Statically add mass in Da to U (iuser_amino_acid)" />
634
635 <param name="add_X_user_amino_acid_bool" type="boolean" checked="true"
636 label="Statically add mass in Da to X (iuser_amino_acid)"/>
637 <param name="add_X_user_amino_acid" type="float" value="0.0"
638 label="Statically add mass in Da to X (iuser_amino_acid)" />
639
640 <param name="add_Z_user_amino_acid_bool" type="boolean" checked="true"
641 label="Statically add mass in Da to Z (iuser_amino_acid)"/>
642 <param name="add_Z_user_amino_acid" type="float" value="0.0"
643 label="Statically add mass in Da to Z (iuser_amino_acid)" />
544 </section> 644 </section>
545 </xml> 645 </xml>
546 <token name="@STATIC_MODIFICATION@"><![CDATA[ 646 <token name="@STATIC_MODIFICATION@"><![CDATA[
547 #set $fmods = {} 647 #set $fmod_vals = {}
548 #if $prefix.static_modification.add_Cterm_peptide != '' 648 #set $fmod_vals['add_Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide
549 #set $fmods['Cterm_peptide'] = $prefix.static_modification.add_Cterm_peptide 649 #set $fmod_vals['add_Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide
550 #end if 650 #set $fmod_vals['add_Cterm_protein'] = $prefix.static_modification.add_Cterm_protein
551 #if $prefix.static_modification.add_Nterm_peptide != '' 651 #set $fmod_vals['add_Nterm_protein'] = $prefix.static_modification.add_Nterm_protein
552 #set $fmods['Nterm_peptide'] = $prefix.static_modification.add_Nterm_peptide 652 #set $fmod_vals['add_G_glycine'] = $prefix.static_modification.add_G_glycine
553 #end if 653 #set $fmod_vals['add_A_alanine'] = $prefix.static_modification.add_A_alanine
554 #if $prefix.static_modification.add_Cterm_protein != '' 654 #set $fmod_vals['add_S_serine'] = $prefix.static_modification.add_S_serine
555 #set $fmods['Cterm_protein'] = $prefix.static_modification.add_Cterm_protein 655 #set $fmod_vals['add_P_proline'] = $prefix.static_modification.add_P_proline
556 #end if 656 #set $fmod_vals['add_V_valine'] = $prefix.static_modification.add_V_valine
557 #if $prefix.static_modification.add_Nterm_protein != '' 657 #set $fmod_vals['add_T_threonine'] = $prefix.static_modification.add_T_threonine
558 #set $fmods['Nterm_protein'] = $prefix.static_modification.add_Nterm_protein 658 #set $fmod_vals['add_C_cysteine'] = $prefix.static_modification.add_C_cysteine
559 #end if 659 #set $fmod_vals['add_L_leucine'] = $prefix.static_modification.add_L_leucine
560 #if $prefix.static_modification.add_G_glycine != '' 660 #set $fmod_vals['add_I_isoleucine'] = $prefix.static_modification.add_I_isoleucine
561 #set $fmods['G_glycine'] = $prefix.static_modification.add_G_glycine 661 #set $fmod_vals['add_N_asparagine'] = $prefix.static_modification.add_N_asparagine
562 #end if 662 #set $fmod_vals['add_D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid
563 #if $prefix.static_modification.add_A_alanine != '' 663 #set $fmod_vals['add_Q_glutamine'] = $prefix.static_modification.add_Q_glutamine
564 #set $fmods['A_alanine'] = $prefix.static_modification.add_A_alanine 664 #set $fmod_vals['add_K_lysine'] = $prefix.static_modification.add_K_lysine
565 #end if 665 #set $fmod_vals['add_E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid
566 #if $prefix.static_modification.add_S_serine != '' 666 #set $fmod_vals['add_M_methionine'] = $prefix.static_modification.add_M_methionine
567 #set $fmods['S_serine'] = $prefix.static_modification.add_S_serine 667 #set $fmod_vals['add_H_histidine'] = $prefix.static_modification.add_H_histidine
568 #end if 668 #set $fmod_vals['add_F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine
569 #if $prefix.static_modification.add_P_proline != '' 669 #set $fmod_vals['add_R_arginine'] = $prefix.static_modification.add_R_arginine
570 #set $fmods['P_proline'] = $prefix.static_modification.add_P_proline 670 #set $fmod_vals['add_Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine
571 #end if 671 #set $fmod_vals['add_W_tryptophan'] = $prefix.static_modification.add_W_tryptophan
572 #if $prefix.static_modification.add_V_valine != '' 672 #set $fmod_vals['add_B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid
573 #set $fmods['V_valine'] = $prefix.static_modification.add_V_valine 673 #set $fmod_vals['add_J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid
574 #end if 674 #set $fmod_vals['add_O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid
575 #if $prefix.static_modification.add_T_threonine != '' 675 #set $fmod_vals['add_U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid
576 #set $fmods['T_threonine'] = $prefix.static_modification.add_T_threonine 676 #set $fmod_vals['add_X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid
577 #end if 677 #set $fmod_vals['add_Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid
578 #if $prefix.static_modification.add_C_cysteine != '' 678
579 #set $fmods['C_cysteine'] = $prefix.static_modification.add_C_cysteine 679 #set $fmod_bools = {}
580 #end if 680 #set $fmod_bools['add_Cterm_peptide_bool'] = $prefix.static_modification.add_Cterm_peptide_bool
581 #if $prefix.static_modification.add_L_leucine != '' 681 #set $fmod_bools['add_Nterm_peptide_bool'] = $prefix.static_modification.add_Nterm_peptide_bool
582 #set $fmods['L_leucine'] = $prefix.static_modification.add_L_leucine 682 #set $fmod_bools['add_Cterm_protein_bool'] = $prefix.static_modification.add_Cterm_protein_bool
583 #end if 683 #set $fmod_bools['add_Nterm_protein_bool'] = $prefix.static_modification.add_Nterm_protein_bool
584 #if $prefix.static_modification.add_I_isoleucine != '' 684 #set $fmod_bools['add_G_glycine_bool'] = $prefix.static_modification.add_G_glycine_bool
585 #set $fmods['I_isoleucine'] = $prefix.static_modification.add_I_isoleucine 685 #set $fmod_bools['add_A_alanine_bool'] = $prefix.static_modification.add_A_alanine_bool
586 #end if 686 #set $fmod_bools['add_S_serine_bool'] = $prefix.static_modification.add_S_serine_bool
587 #if $prefix.static_modification.add_N_asparagine != '' 687 #set $fmod_bools['add_P_proline_bool'] = $prefix.static_modification.add_P_proline_bool
588 #set $fmods['N_asparagine'] = $prefix.static_modification.add_N_asparagine 688 #set $fmod_bools['add_V_valine_bool'] = $prefix.static_modification.add_V_valine_bool
589 #end if 689 #set $fmod_bools['add_T_threonine_bool'] = $prefix.static_modification.add_T_threonine_bool
590 #if $prefix.static_modification.add_D_aspartic_acid != '' 690 #set $fmod_bools['add_C_cysteine_bool'] = $prefix.static_modification.add_C_cysteine_bool
591 #set $fmods['D_aspartic_acid'] = $prefix.static_modification.add_D_aspartic_acid 691 #set $fmod_bools['add_L_leucine_bool'] = $prefix.static_modification.add_L_leucine_bool
592 #end if 692 #set $fmod_bools['add_I_isoleucine_bool'] = $prefix.static_modification.add_I_isoleucine_bool
593 #if $prefix.static_modification.add_Q_glutamine != '' 693 #set $fmod_bools['add_N_asparagine_bool'] = $prefix.static_modification.add_N_asparagine_bool
594 #set $fmods['Q_glutamine'] = $prefix.static_modification.add_Q_glutamine 694 #set $fmod_bools['add_D_aspartic_acid_bool'] = $prefix.static_modification.add_D_aspartic_acid_bool
595 #end if 695 #set $fmod_bools['add_Q_glutamine_bool'] = $prefix.static_modification.add_Q_glutamine_bool
596 #if $prefix.static_modification.add_K_lysine != '' 696 #set $fmod_bools['add_K_lysine_bool'] = $prefix.static_modification.add_K_lysine_bool
597 #set $fmods['K_lysine'] = $prefix.static_modification.add_K_lysine 697 #set $fmod_bools['add_E_glutamic_acid_bool'] = $prefix.static_modification.add_E_glutamic_acid_bool
598 #end if 698 #set $fmod_bools['add_M_methionine_bool'] = $prefix.static_modification.add_M_methionine_bool
599 #if $prefix.static_modification.add_E_glutamic_acid != '' 699 #set $fmod_bools['add_H_histidine_bool'] = $prefix.static_modification.add_H_histidine_bool
600 #set $fmods['E_glutamic_acid'] = $prefix.static_modification.add_E_glutamic_acid 700 #set $fmod_bools['add_F_phenylalanine_bool'] = $prefix.static_modification.add_F_phenylalanine_bool
601 #end if 701 #set $fmod_bools['add_R_arginine_bool'] = $prefix.static_modification.add_R_arginine_bool
602 #if $prefix.static_modification.add_M_methionine != '' 702 #set $fmod_bools['add_Y_tyrosine_bool'] = $prefix.static_modification.add_Y_tyrosine_bool
603 #set $fmods['M_methionine'] = $prefix.static_modification.add_M_methionine 703 #set $fmod_bools['add_W_tryptophan_bool'] = $prefix.static_modification.add_W_tryptophan_bool
604 #end if 704 #set $fmod_bools['add_B_user_amino_acid_bool'] = $prefix.static_modification.add_B_user_amino_acid_bool
605 #if $prefix.static_modification.add_H_histidine != '' 705 #set $fmod_bools['add_J_user_amino_acid_bool'] = $prefix.static_modification.add_J_user_amino_acid_bool
606 #set $fmods['H_histidine'] = $prefix.static_modification.add_H_histidine 706 #set $fmod_bools['add_O_user_amino_acid_bool'] = $prefix.static_modification.add_O_user_amino_acid_bool
607 #end if 707 #set $fmod_bools['add_U_user_amino_acid_bool'] = $prefix.static_modification.add_U_user_amino_acid_bool
608 #if $prefix.static_modification.add_F_phenylalanine != '' 708 #set $fmod_bools['add_X_user_amino_acid_bool'] = $prefix.static_modification.add_X_user_amino_acid_bool
609 #set $fmods['F_phenylalanine'] = $prefix.static_modification.add_F_phenylalanine 709 #set $fmod_bools['add_Z_user_amino_acid_bool'] = $prefix.static_modification.add_Z_user_amino_acid_bool
610 #end if 710
611 #if $prefix.static_modification.add_R_arginine != ''
612 #set $fmods['R_arginine'] = $prefix.static_modification.add_R_arginine
613 #end if
614 #if $prefix.static_modification.add_Y_tyrosine != ''
615 #set $fmods['Y_tyrosine'] = $prefix.static_modification.add_Y_tyrosine
616 #end if
617 #if $prefix.static_modification.add_W_tryptophan != ''
618 #set $fmods['W_tryptophan'] = $prefix.static_modification.add_W_tryptophan
619 #end if
620 #*
621 #if $prefix.static_modification.add_B_user_amino_acid != ''
622 #set $fmods['B_user_amino_acid'] = $prefix.static_modification.add_B_user_amino_acid
623 #end if
624 #if $prefix.static_modification.add_J_user_amino_acid != ''
625 #set $fmods['J_user_amino_acid'] = $prefix.static_modification.add_J_user_amino_acid
626 #end if
627 #if $prefix.static_modification.add_O_user_amino_acid != ''
628 #set $fmods['O_user_amino_acid'] = $prefix.static_modification.add_O_user_amino_acid
629 #end if
630 #if $prefix.static_modification.add_U_user_amino_acid != ''
631 #set $fmods['U_user_amino_acid'] = $prefix.static_modification.add_U_user_amino_acid
632 #end if
633 #if $prefix.static_modification.add_X_user_amino_acid != ''
634 #set $fmods['X_user_amino_acid'] = $prefix.static_modification.add_X_user_amino_acid
635 #end if
636 #if $prefix.static_modification.add_Z_user_amino_acid != ''
637 #set $fmods['Z_user_amino_acid'] = $prefix.static_modification.add_Z_user_amino_acid
638 #end if
639 *#
640 ]]></token> 711 ]]></token>
641 712
642 <xml name="spectrum_processing" token_mode_selected="false" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false"> 713 <xml name="spectrum_processing" token_mode_selected="true" token_mode_isolated="false" token_mode_corrected="false" token_override_charge="false" token_rm_peak0="false" token_rm_peak1="true" token_rm_peak2="false" token_clear_mz_range_min="0.0" token_clear_mz_range_max="0.0" token_transform_none="true" token_transform_sqrt="false" token_check_spectral_files="true">
643 <section name="spectrum_processing" expanded="false" title="Spectrum Processing"> 714 <section name="spectrum_processing" expanded="false" title="Spectrum Processing">
644 <param name="precursor_mass_mode" type="select" optional="true" label="Precursor mass mode"> 715 <param name="precursor_mass_mode" type="select" label="Precursor mass mode">
645 <option value="isolated" selected="@MODE_ISOLATED@">isolated</option> 716 <option value="isolated" selected="@MODE_ISOLATED@">isolated</option>
646 <option value="selected" selected="@MODE_SELECTED@">selected</option> 717 <option value="selected" selected="@MODE_SELECTED@">selected</option>
647 <option value="corrected" selected="@MODE_CORRECTED@">corrected</option> 718 <option value="corrected" selected="@MODE_CORRECTED@">corrected</option>
648 </param> 719 </param>
649 <param name="minimum_peaks" type="integer" value="" min="0" optional="true" 720 <param name="minimum_peaks" type="integer" value="" min="0" optional="true"
681 <param name="remove_precursor_range_max" type="float" value="1.5" min="0.0" max="10.0" optional="true" label="Maximum of precursor m/z range to remove" /> 752 <param name="remove_precursor_range_max" type="float" value="1.5" min="0.0" max="10.0" optional="true" label="Maximum of precursor m/z range to remove" />
682 <param name="intensity_transform" type="select" label="Intensity transform"> 753 <param name="intensity_transform" type="select" label="Intensity transform">
683 <option value="0" selected="@TRANSFORM_NONE@">None, not removed</option> 754 <option value="0" selected="@TRANSFORM_NONE@">None, not removed</option>
684 <option value="1" selected="@TRANSFORM_SQRT@">Square root</option> 755 <option value="1" selected="@TRANSFORM_SQRT@">Square root</option>
685 </param> 756 </param>
686 <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Check spectral files"/> 757 <param name="check_spectral_files" type="boolean" truevalue="true" falsevalue="false" checked="@CHECK_SPECTRAL_FILES@" label="Check spectral files"/>
687 <param name="require_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require precursor"/> 758 <param name="require_precursor" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Require precursor"/>
688 <param name="reuse_dia_fragment_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Reuse DIA fragment peaks"/> 759 <param name="reuse_dia_fragment_peaks" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Reuse DIA fragment peaks"/>
689 <param name="activation_types" type="select" optional="true" label="Activation Type Filter"> 760 <param name="activation_types" type="select" optional="true" label="Activation Type Filter">
690 <option value="all" selected="true">all</option> 761 <option value="all" selected="true">all</option>
691 <option value="HCD">HCD</option> 762 <option value="HCD">HCD</option>
768 label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value." 839 label="Ranks a zero-bin hit above all non-zero-bin hit if it has expectation less than this value."
769 help="Default: 0.0" /> 840 help="Default: 0.0" />
770 <param name="zero_bin_mult_expect" type="float" value="" min="0.0" optional="true" 841 <param name="zero_bin_mult_expect" type="float" value="" min="0.0" optional="true"
771 label="Multiplies expect value of PSMs in the zero-bin during results ordering" 842 label="Multiplies expect value of PSMs in the zero-bin during results ordering"
772 help="(set to less than 1 for boosting) Default: 1.0" /> 843 help="(set to less than 1 for boosting) Default: 1.0" />
773 <param name="add_topN_complementary" type="integer" value="" min="0" optional="true"
774 label="Insert complementary ions corresponding to the top N most intense fragments in each experimental spectra." >
775 <help>
776 Useful for recovery of modified peptides near C-terminal in open search.
777 Should be set to 0 (disabled) otherwise.
778 Default: 0
779 </help>
780 </param>
781 <param name="delta_mass_exclude_ranges_min" type="float" value="-1.5" label="Delta mass exclude range minimum" /> 844 <param name="delta_mass_exclude_ranges_min" type="float" value="-1.5" label="Delta mass exclude range minimum" />
782 <param name="delta_mass_exclude_ranges_max" type="float" value="3.5" label="Delta mass exclude range maximum" /> 845 <param name="delta_mass_exclude_ranges_max" type="float" value="3.5" label="Delta mass exclude range maximum" />
783 <param name="localize_delta_mass" type="boolean" truevalue="true" falsevalue="false" checked="@LOCALIZE@" 846 <param name="localize_delta_mass" type="boolean" truevalue="true" falsevalue="false" checked="@LOCALIZE@"
784 label="Localize mass shift (LOS)"/> 847 label="Localize mass shift (LOS)"/>
785 </section> 848 </section>
795 #if $prefix.open_search.zero_bin_accept_expect != '' 858 #if $prefix.open_search.zero_bin_accept_expect != ''
796 #set $msfragger_dict['zero_bin_accept_expect'] = $prefix.open_search.zero_bin_accept_expect 859 #set $msfragger_dict['zero_bin_accept_expect'] = $prefix.open_search.zero_bin_accept_expect
797 #end if 860 #end if
798 #if $prefix.open_search.zero_bin_mult_expect != '' 861 #if $prefix.open_search.zero_bin_mult_expect != ''
799 #set $msfragger_dict['zero_bin_mult_expect'] = $prefix.open_search.zero_bin_mult_expect 862 #set $msfragger_dict['zero_bin_mult_expect'] = $prefix.open_search.zero_bin_mult_expect
800 #end if
801 #if $prefix.open_search.add_topN_complementary != ''
802 #set $msfragger_dict['add_topN_complementary'] = $prefix.open_search.add_topN_complementary
803 #end if 863 #end if
804 #set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass 864 #set $msfragger_dict['localize_delta_mass'] = $prefix.open_search.localize_delta_mass
805 #set $msfragger_dict['delta_mass_exclude_ranges'] = '(' + ','.join([str($prefix.open_search.delta_mass_exclude_ranges_min),str($prefix.open_search.delta_mass_exclude_ranges_max)]) + ')' 865 #set $msfragger_dict['delta_mass_exclude_ranges'] = '(' + ','.join([str($prefix.open_search.delta_mass_exclude_ranges_min),str($prefix.open_search.delta_mass_exclude_ranges_max)]) + ')'
806 ]]></token> 866 ]]></token>
807 867
936 ]]></token> 996 ]]></token>
937 997
938 <!-- Formatting options for output files. --> 998 <!-- Formatting options for output files. -->
939 <xml name="advanced_options"> 999 <xml name="advanced_options">
940 <section name="advanced_options" expanded="false" title="Advanced Options"> 1000 <section name="advanced_options" expanded="false" title="Advanced Options">
941 <param name="output_format" type="select" multiple="true" label="output format"> 1001 <param name="output_format" type="select" label="output format">
942 <option value="pepXML">PEPXML</option> 1002 <option value="pepXML">PEPXML</option>
943 <option value="tsv">TSV</option> 1003 <option value="tsv">TSV</option>
944 <option value="tsv_pepXML">TSV_PEPXML</option> 1004 <option value="tsv_pepXML">TSV_PEPXML</option>
945 <option value="pin">PIN</option> 1005 <option value="pin">PIN</option>
946 <option value="tsv_pin">TSV_PIN</option> 1006 <option value="tsv_pin">TSV_PIN</option>
953 label="Report alternative proteins"/> 1013 label="Report alternative proteins"/>
954 <param name="output_max_expect" type="float" value="50.0" min="0.0" optional="true" 1014 <param name="output_max_expect" type="float" value="50.0" min="0.0" optional="true"
955 label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" /> 1015 label="Suppresses reporting of PSM if top hit has expectation greater than this threshold" />
956 1016
957 <param name="write_calibrated_mzml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write calibrated mzML"/> 1017 <param name="write_calibrated_mzml" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write calibrated mzML"/>
958 <param name="write_uncalibrated_mgf" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Write uncalibrated MGF"/>
959 <param name="group_variable" type="select" optional="true" label="Group variable"> 1018 <param name="group_variable" type="select" optional="true" label="Group variable">
960 <option value="0">None</option> 1019 <option value="0">None</option>
961 <option value="1">Number of enzymatic termini</option> 1020 <option value="1">Number of enzymatic termini</option>
962 <option value="2">Protein evidence from FASTA file</option> 1021 <option value="2">Protein evidence from FASTA file</option>
963 </param> 1022 </param>
964 </section> 1023 </section>
965 </xml> 1024 </xml>
966 1025
967 <!-- Does not enter into msfragger_dict, instead produces configuration text. --> 1026 <!-- Does not enter into msfragger_dict, instead produces configuration text. -->
968 <token name="@MSFRAGGER_ADVANCED_OPTIONS@"><![CDATA[ 1027 <token name="@MSFRAGGER_ADVANCED_OPTIONS@"><![CDATA[
969 #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format.__str__.replace(',mgf','').replace(',','_') 1028 #set $msfragger_dict['output_format'] = $prefix.advanced_options.output_format
970 #if $prefix.advanced_options.output_report_topN != '' 1029 #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN
971 #set $msfragger_dict['output_report_topN'] = $prefix.advanced_options.output_report_topN
972 #end if
973 #set $msfragger_dict['report_alternative_proteins'] = $prefix.advanced_options.report_alternative_proteins 1030 #set $msfragger_dict['report_alternative_proteins'] = $prefix.advanced_options.report_alternative_proteins
1031 #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect
974 #if $prefix.advanced_options.output_max_expect != '' 1032 #if $prefix.advanced_options.output_max_expect != ''
975 #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect 1033 #set $msfragger_dict['output_max_expect'] = $prefix.advanced_options.output_max_expect
976 #end if 1034 #end if
977 #set $msfragger_dict['write_calibrated_mzml'] = $prefix.advanced_options.write_calibrated_mzml 1035 #set $msfragger_dict['write_calibrated_mzml'] = $prefix.advanced_options.write_calibrated_mzml
978 #set $msfragger_dict['write_uncalibrated_mgf'] = $prefix.advanced_options.write_uncalibrated_mgf
979 #if $prefix.advanced_options.group_variable != 'None' 1036 #if $prefix.advanced_options.group_variable != 'None'
980 #set $msfragger_dict['group_variable'] = $prefix.advanced_options.group_variable 1037 #set $msfragger_dict['group_variable'] = $prefix.advanced_options.group_variable
981 #end if 1038 #end if
982 ]]></token> 1039 ]]></token>
983 1040