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comparison peptide_shaker.xml @ 18:a5f9b959d5d1 draft

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author iracooke
date Wed, 25 Jun 2014 11:49:45 -0400
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17:6cdbfdffb38e 18:a5f9b959d5d1
1 <tool id="peptide_shaker" name="Peptide Shaker" version="1.19.5.0">
2 <description>
3 Perform protein identification using various search engines (using SearchGUI) and combine results with PeptideShaker.
4 </description>
5 <requirements>
6 <requirement type="package" version="0.31.4">peptide_shaker</requirement>
7 <requirement type="package" version="1.19.5">searchgui</requirement>
8 <!--<requirement type="package" version="2.2.29">blast+</requirement>-->
9 </requirements>
10 <stdio>
11 <exit_code range="1:" level="fatal" description="Job Failed" />
12 <regex match="java.*Exception" level="fatal" description="Java Exception"/>
13 <regex match="Could not create the Java virtual machine" level="fatal" description="JVM Error"/>
14 </stdio>
15 <command>
16
17 #from datetime import datetime
18 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
19 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
20 #set $temp_stderr = 'macs2_stderr'
21
22 mkdir output;
23 mkdir output_reports;
24 cwd=`pwd`;
25 #for $mgf in $peak_lists:
26 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
27 ln -s '${mgf}' '${input_name}';
28 #end for
29 ##ln -s "${input_database}" input_database.fasta;
30 cp "${input_database}" input_database.fasta;
31
32 ###########################################
33 #### Creating decoy database ####
34 ###########################################
35 #if $create_decoy:
36 echo "Creating decoy database.";
37 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy;
38 rm input_database.fasta;
39 cp input_database_concatenated_target_decoy.fasta input_database.fasta;
40 ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
41 #end if
42
43 #####################################################
44 ## generate IdentificationParameters for SearchGUI ##
45 #####################################################
46
47 (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
48 -out SEARCHGUI_IdentificationParameters.parameters
49 -prec_ppm "${precursor_ion_tol_units}"
50 -prec_tol "${precursor_ion_tol}"
51 -frag_tol "${fragment_tol}"
52 -enzyme "${enzyme}"
53 #set $fixed_mods_str = $fixed_modifications or ''
54 #set $variable_mods_str = $variable_modifications or ''
55 #if $fixed_mods_str
56 -fixed_mods "${fixed_mods_str}"
57 #end if
58 #if $variable_mods_str
59 -variable_mods "${variable_mods_str}"
60 #end if
61 -min_charge "${min_charge}"
62 -max_charge "${max_charge}"
63 -mc "${missed_cleavages}"
64 -fi "${forward_ion}"
65 -ri "${reverse_ion}"
66 -db input_database.fasta
67
68 #if $advanced.advanced_type_selector == "advanced":
69
70 #if $advanced.xtandem.xtandem_selector == "yes"
71
72 -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
73 -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
74 -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
75 -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
76 -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
77
78 #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
79 -xtandem_refine 1
80 -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
81 -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
82 -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
83 -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
84 -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
85 #end if
86 #end if
87
88 #if $advanced.omssa.omssa_selector == "yes"
89 -omssa_hitlist_length ${advanced.omssa.hitlist_length}
90 -omssa_remove_prec ${advanced.omssa.remove_precursor}
91 -omssa_scale_prec ${advanced.omssa.scale_precursor}
92 -omssa_estimate_charge ${advanced.omssa.estimate_charge}
93 #end if
94
95 #if $advanced.msgf.msgf_selector == "yes"
96 -msgf_decoy ${advanced.msgf.msgf_decoy}
97 -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
98 -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
99 -msgf_termini ${advanced.msgf.msgf_termini}
100 -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
101 #end if
102
103 ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
104 ##end if
105
106 #end if
107
108 2> $temp_stderr)
109 &amp;&amp;
110
111 ################
112 ## Search CLI ##
113 ################
114 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
115 -temp_folder `pwd`
116 -spectrum_files \$cwd
117 -output_folder \$cwd/output
118 -id_params SEARCHGUI_IdentificationParameters.parameters
119
120 -threads "\${GALAXY_SLOTS:-12}"
121 -correct_titles "${correct_titles}"
122 $missing_titles
123 -mgf_splitting "${mgf_splitting}"
124 -mgf_spectrum_count "${mgf_spectrum_count}"
125
126 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
127 ## the tree is generated afterwards in PeptideShaker
128 -protein_index 0
129
130 ##-makeblastdb_folder \$BLAST_ROOT_DIR
131
132 #if $advanced.advanced_type_selector == "advanced":
133
134 #if $advanced.xtandem.xtandem_selector == "yes"
135 -xtandem 1
136 #else
137 -xtandem 0
138 #end if
139
140 #if $advanced.omssa.omssa_selector == "yes"
141 -omssa 1
142 #else
143 -omssa 0
144 #end if
145
146 #if $advanced.msgf.msgf_selector == "yes"
147 -msgf 1
148 #else
149 -msgf 0
150 #end if
151
152 #if $advanced.ms_amanda.ms_amanda_selector == "yes"
153 -ms_amanda 1
154 #else
155 -ms_amanda 0
156 #end if
157
158 #else
159 -ms_amanda 0
160 #end if
161
162 2>> $temp_stderr)
163 &amp;&amp;
164
165 #########################################################
166 ## generate IdentificationParameters for PeptideShaker ##
167 #########################################################
168 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.IdentificationParametersCLI
169 -out PEPTIDESHAKER_IdentificationParameters.parameters
170 -prec_ppm "${precursor_ion_tol_units}"
171 -prec_tol "${precursor_ion_tol}"
172 -frag_tol "${fragment_tol}"
173 -enzyme "${enzyme}"
174 #set $fixed_mods_str = $fixed_modifications or ''
175 #set $variable_mods_str = $variable_modifications or ''
176 #if $fixed_mods_str
177 -fixed_mods "$fixed_mods_str"
178 #end if
179 #if $variable_mods_str
180 -variable_mods "$variable_mods_str"
181 #end if
182 -min_charge $min_charge
183 -max_charge $max_charge
184 -mc $missed_cleavages
185 -fi $forward_ion
186 -ri $reverse_ion
187 -db input_database.fasta
188
189 2>> $temp_stderr)
190 &amp;&amp;
191
192 ######################
193 ## PeptideShakerCLI ##
194 ######################
195 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.PeptideShakerCLI
196 -temp_folder `pwd`
197 -experiment '${exp_str}'
198 -sample '${samp_str}'
199 -replicate 1
200 -spectrum_files \$cwd
201 -identification_files \$cwd/output
202 -out \$cwd/peptide_shaker_output.cps
203 -id_params PEPTIDESHAKER_IdentificationParameters.parameters
204
205 ##Optional gene annotation parameter
206 #if $species_type.species_type_selector != 'no_species_type':
207 -species_type "${species_type.species_type_selector}"
208 -species "${species_type.species}"
209 #end if
210
211 ##Optional processing parameters:
212 #if $processing_options.processing_options_selector == "yes"
213 -protein_FDR "${processing_options.protein_fdr}"
214 -peptide_FDR "${processing_options.peptide_fdr}"
215 -psm_FDR "${processing_options.psm_fdr}"
216 -ptm_score "${processing_options.ptm_score.ptm_score_selector}"
217 #if $processing_options.ptm_score.ptm_score_selector == 1
218 -score_neutral_losses "${processing_options.ptm_score.neutral_losses}"
219 #if str($processing_options.ptm_score.ptm_threshold) != ''
220 -ptm_threshold "${processing_options.ptm_score.ptm_threshold}"
221 #end if
222 #end if
223 -protein_fraction_mw_confidence "${processing_options.protein_fraction_mw_confidence}"
224 #end if
225
226 ##Optional filtering parameters:
227 #if $filtering_options.filtering_options_selector == "yes":
228 -min_peptide_length "${filtering_options.min_peptide_length}"
229 -max_peptide_length "${filtering_options.max_peptide_length}"
230 -max_precursor_error "${filtering_options.max_precursor_error}"
231 -max_precursor_error_type "${filtering_options.max_precursor_error_type}"
232 -max_xtandem_e "${filtering_options.max_xtandem_e}"
233 -max_omssa_e "${filtering_options.max_omssa_e}"
234 -max_mascot_e "${filtering_options.max_mascot_e}"
235 -exclude_unknown_ptms "${filtering_options.exclude_unknown_ptms}"
236 #end if
237
238 2>> $temp_stderr)
239 &amp;&amp;
240
241 ##################################
242 ## PeptideShaker Report options ##
243 ##################################
244 (java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.ReportCLI
245 -temp_folder `pwd`
246 -in \$cwd/peptide_shaker_output.cps
247 -out_reports \$cwd/output_reports
248 #set $cleaned_list = str($outputs).split(',')
249 #if 'cps' in $cleaned_list:
250 #silent $cleaned_list.remove('cps')
251 #end if
252 #if 'mzidentML' in $cleaned_list:
253 #silent $cleaned_list.remove('mzidentML')
254 #end if
255 -reports #echo ','.join($cleaned_list)#
256
257 2>> $temp_stderr)
258 &amp;&amp;
259
260 #if 'mzidentML' in str($outputs).split(','):
261 java -cp \$PEPTIDESHAKER_JAR_PATH eu.isas.peptideshaker.cmd.MzidCLI
262 -in \$cwd/peptide_shaker_output.cps
263 -output_file output.mzid
264 -contact_first_name 'Proteomics'
265 -contact_last_name 'Galaxy'
266 -contact_email 'galaxyp@umn.edu'
267 -contact_address 'galaxyp@umn.edu'
268 -organization_name 'University of Minnesota'
269 -organization_email 'galaxyp@umn.edu'
270 -organization_address 'Minneapolis, MN 55455, Vereinigte Staaten'
271 ;
272 #end if
273 #if '0' in str($outputs).split(','):
274 find \$cwd/output_reports -name '*Certificate*' -exec bash -c 'mv "$0" "certificate.txt"' {} \;
275 ;
276 #end if
277 #if '2' in str($outputs).split(','):
278 find \$cwd/output_reports -name '*PSM*' -exec bash -c 'mv "$0" "psm.txt"' {} \;
279 ;
280 #end if
281 #if '3' in str($outputs).split(','):
282 find \$cwd/output_reports -name '*Peptide*' -exec bash -c 'mv "$0" "peptides.txt"' {} \;
283 ;
284 #end if
285 #if '4' in str($outputs).split(','):
286 find \$cwd/output_reports -name '*Protein*' -exec bash -c 'mv "$0" "proteins.txt"' {} \;
287 ;
288 #end if
289 #if '1' in str($outputs).split(','):
290 find \$cwd/output_reports -name '*Hierarchical*' -exec bash -c 'mv "$0" "hierarchical.txt"' {} \;
291 ;
292 #end if
293
294 exit_code_for_galaxy=\$?;
295 cat $temp_stderr 2&gt;&amp;1;
296 (exit \$exit_code_for_galaxy)
297
298 </command>
299 <inputs>
300 <param format="fasta" name="input_database" type="data" label="Protein Database"
301 help="Select FASTA database from history"/>
302
303 <param name="create_decoy" label="Create a concatenated target/decoy database before running PeptideShaker." type="boolean" truevalue="True" falsevalue="False" checked="true" help="Selecting this option will help PeptideShaker calculate FDR values" />
304
305 <param format="mgf" name="peak_lists" type="data" multiple="true" label="Input Peak Lists (mgf)"
306 help="Select appropriate MGF dataset(s) from history" />
307 <param name="precursor_ion_tol_units" type="select" label="Precursor Ion Tolerance Units"
308 help="Select based on instrument used, as different machines provide different quality of spectra. ppm is a standard for most precursor ions">
309 <option value="1">Parts per million (ppm)</option>
310 <option value="0">Daltons</option>
311 </param>
312 <param name="precursor_ion_tol" type="float" value="10" label="Percursor Ion Tolerance"
313 help="Provide error value for precursor ion, based on instrument used. 10 ppm recommended for Orbitrap instrument"/>
314 <param name="fragment_tol" type="float" value="0.5" label="Fragment Tolerance (Daltons)"
315 help="Provide error value for fragment ions, based on instrument used"/>
316 <param name="enzyme" type="select" label="Enzyme"
317 help="Which enzyme was used for protein digest in experiment? In most cases, trypsin is used">
318 <option value="Trypsin">Trypsin</option>
319 <option value="Arg-C">Arg-C</option>
320 <option value="CNBr">CNBr</option>
321 <option value="Chymotrypsin (FYWL)">Chymotrypsin (FYWL)</option>
322 <option value="Formic Acid">Formic Acid</option>
323 <option value="Lys-C">Lys-C</option>
324 <option value="Lys-C, no P rule">Lys-C, no P rule</option>
325 <option value="Pepsin A">Pepsin A</option>
326 <option value="Trypsin + CNBr">Trypsin + CNBr</option>
327 <option value="Trypsin + Chymotrypsin (FYWLKR)">Trypsin + Chymotrypsin (FYWLKR)</option>
328 <option value="Trypsin, no P rule">Trypsin, no P rule</option>
329 <option value="whole protein">whole protein</option>
330 <option value="Asp-N">Asp-N</option>
331 <option value="Glu-C">Glu-C</option>
332 <option value="Asp-N + Glu-C">Asp-N + Glu-C</option>
333 <option value="Top-Down">Top-Down</option>
334 <option value="Semi-Tryptic">Semi-Tryptic</option>
335 <option value="No enzyme">No enzyme</option>
336 <option value="Chymotrypsin, no P rule (FYWL)">Chymotrypsin, no P rule (FYWL)</option>
337 <option value="Asp-N (DE)">Asp-N (DE)</option>
338 <option value="Glu-C (DE)">Glu-C (DE)</option>
339 <option value="Lys-N (K)">Lys-N (K)</option>
340 <option value="Thermolysin, no P rule">Thermolysin, no P rule</option>
341 <option value="Semi-Chymotrypsin (FYWL)">Semi-Chymotrypsin (FYWL)</option>
342 <option value="Semi-Glu-C">Semi-Glu-C</option>
343 </param>
344
345 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
346 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
347 <option value="0">no correction</option>
348 <option value="1" selected="True">rename spectra</option>
349 <option value="2">delete spectra</option>
350 </param>
351
352 <param name="missing_titles" label="Add missing spectrum titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" help="(-missing_titles)"/>
353
354 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
355 help="Choose a smaller value if you are running on a machine with limited memory"/>
356 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
357 help="Choose a smaller value if you are running on a machine with limited memory"/>
358
359 <conditional name="species_type">
360 <param name="species_type_selector" type="select" optional="true" label="The species type to use for the gene annotation"
361 help="(Optional) If your species is supported under one of the groups, selecting it will allow GO annotations and other information to be included in the results">
362 <option value="Fungi">Fungi</option>
363 <option value="Plants">Plants</option>
364 <option value="Metazoa">Metazoa</option>
365 <option value="Vertebrates">Vertebrates</option>
366 <option value="Protists">Protists</option>
367 <option value="no_species_type" selected="true">No species restriction</option>
368 </param>
369 <when value="Protists">
370 <param name="species" type="select" label="The species to use for the gene annotation"
371 help="">
372 <option value="Albugo laibachii">Albugo laibachii</option>
373 <option value="Dictyostelium discoideum">Dictyostelium discoideum</option>
374 <option value="Entamoeba histolytica">Entamoeba histolytica</option>
375 <option value="Giardia lamblia">Giardia lamblia</option>
376 <option value="Guillardia theta CCMP2712">Guillardia theta CCMP2712</option>
377 <option value="Hyaloperonospora arabidopsidis">Hyaloperonospora arabidopsidis</option>
378 <option value="Leishmania major">Leishmania major</option>
379 <option value="Phaeodactylum tricornutum">Phaeodactylum tricornutum</option>
380 <option value="Phytophthora infestans">Phytophthora infestans</option>
381 <option value="Phytophthora ramorum">Phytophthora ramorum</option>
382 <option value="Phytophthora sojae">Phytophthora sojae</option>
383 <option value="Plasmodium berghei">Plasmodium berghei</option>
384 <option value="Plasmodium chabaudi">Plasmodium chabaudi</option>
385 <option value="Plasmodium falciparum">Plasmodium falciparum</option>
386 <option value="Plasmodium knowlesi">Plasmodium knowlesi</option>
387 <option value="Plasmodium vivax">Plasmodium vivax</option>
388 <option value="Pythium ultimum">Pythium ultimum</option>
389 <option value="Tetrahymena thermophila">Tetrahymena thermophila</option>
390 <option value="Thalassiosira pseudonana">Thalassiosira pseudonana</option>
391 <option value="Toxoplasma gondii">Toxoplasma gondii</option>
392 <option value="Trypanosoma brucei">Trypanosoma brucei</option>
393 </param>
394 </when>
395 <when value="Plants">
396 <param name="species" type="select" label="The species to use for the gene annotation"
397 help="">
398 <option value="Arabidopsis lyrata">Arabidopsis lyrata</option>
399 <option value="Arabidopsis thaliana">Arabidopsis thaliana</option>
400 <option value="Brachypodium distachyon">Brachypodium distachyon</option>
401 <option value="Brassica rapa genes">Brassica rapa genes</option>
402 <option value="Chlamydomonas reinhardtii">Chlamydomonas reinhardtii</option>
403 <option value="Cyanidioschyzon merolae">Cyanidioschyzon merolae</option>
404 <option value="Glycine max">Glycine max</option>
405 <option value="Hordeum vulgare">Hordeum vulgare</option>
406 <option value="Medicago truncatula">Medicago truncatula</option>
407 <option value="Musa acuminata">Musa acuminata</option>
408 <option value="Oryza brachyantha">Oryza brachyantha</option>
409 <option value="Oryza glaberrima">Oryza glaberrima</option>
410 <option value="Oryza sativa Indica Group">Oryza sativa Indica Group</option>
411 <option value="Oryza sativa">Oryza sativa</option>
412 <option value="Physcomitrella patens">Physcomitrella patens</option>
413 <option value="Populus trichocarpa">Populus trichocarpa</option>
414 <option value="Selaginella moellendorffii">Selaginella moellendorffii</option>
415 <option value="Setaria italica">Setaria italica</option>
416 <option value="Solanum lycopersicum">Solanum lycopersicum</option>
417 <option value="Solanum tuberosum">Solanum tuberosum</option>
418 <option value="Sorghum bicolor">Sorghum bicolor</option>
419 <option value="Vitis vinifera">Vitis vinifera</option>
420 <option value="Zea mays">Zea mays</option>
421 </param>
422 </when>
423 <when value="Metazoa">
424 <param name="species" type="select" label="The species to use for the gene annotation"
425 help="">
426 <option value="Acyrthosiphon pisum">Acyrthosiphon pisum</option>
427 <option value="Aedes aegypti">Aedes aegypti</option>
428 <option value="Amphimedon queenslandica">Amphimedon queenslandica</option>
429 <option value="Anopheles darlingi">Anopheles darlingi</option>
430 <option value="Anopheles gambiae">Anopheles gambiae</option>
431 <option value="Apis mellifera">Apis mellifera</option>
432 <option value="Atta cephalotes">Atta cephalotes</option>
433 <option value="Bombyx mori">Bombyx mori</option>
434 <option value="Brugia malayi">Brugia malayi</option>
435 <option value="Caenorhabditis brenneri">Caenorhabditis brenneri</option>
436 <option value="Caenorhabditis briggsae">Caenorhabditis briggsae</option>
437 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
438 <option value="Caenorhabditis japonica">Caenorhabditis japonica</option>
439 <option value="Caenorhabditis remanei">Caenorhabditis remanei</option>
440 <option value="Culex quinquefasciatus">Culex quinquefasciatus</option>
441 <option value="Danaus plexippus">Danaus plexippus</option>
442 <option value="Daphnia pulex">Daphnia pulex</option>
443 <option value="Drosophila ananassae">Drosophila ananassae</option>
444 <option value="Drosophila erecta">Drosophila erecta</option>
445 <option value="Drosophila grimshawi">Drosophila grimshawi</option>
446 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
447 <option value="Drosophila mojavensis">Drosophila mojavensis</option>
448 <option value="Drosophila persimilis">Drosophila persimilis</option>
449 <option value="Drosophila pseudoobscura">Drosophila pseudoobscura</option>
450 <option value="Drosophila sechellia">Drosophila sechellia</option>
451 <option value="Drosophila simulans">Drosophila simulans</option>
452 <option value="Drosophila virilis">Drosophila virilis</option>
453 <option value="Drosophila willistoni">Drosophila willistoni</option>
454 <option value="Drosophila yakuba">Drosophila yakuba</option>
455 <option value="Heliconius melpomene">Heliconius melpomene</option>
456 <option value="Ixodes scapularis">Ixodes scapularis</option>
457 <option value="Loa loa">Loa loa</option>
458 <option value="Megaselia scalaris">Megaselia scalaris</option>
459 <option value="Nasonia vitripennis">Nasonia vitripennis</option>
460 <option value="Nematostella vectensis">Nematostella vectensis</option>
461 <option value="Pediculus humanus">Pediculus humanus</option>
462 <option value="Pristionchus pacificus">Pristionchus pacificus</option>
463 <option value="Schistosoma mansoni">Schistosoma mansoni</option>
464 <option value="Strigamia maritima">Strigamia maritima</option>
465 <option value="Strongylocentrotus purpuratus">Strongylocentrotus purpuratus</option>
466 <option value="Tribolium castaneum">Tribolium castaneum</option>
467 <option value="Trichinella spiralis">Trichinella spiralis</option>
468 <option value="Trichoplax adhaerens">Trichoplax adhaerens</option>
469 </param>
470 </when>
471 <when value="Fungi">
472 <param name="species" type="select" label="The species to use for the gene annotation"
473 help="">
474 <option value="Ashbya gossypii">Ashbya gossypii</option>
475 <option value="Aspergillus clavatus">Aspergillus clavatus</option>
476 <option value="Aspergillus flavus">Aspergillus flavus</option>
477 <option value="Aspergillus fumigatus">Aspergillus fumigatus</option>
478 <option value="Aspergillus fumigatusa1163">Aspergillus fumigatusa1163</option>
479 <option value="Aspergillus nidulans">Aspergillus nidulans</option>
480 <option value="Aspergillus niger">Aspergillus niger</option>
481 <option value="Aspergillus oryzae">Aspergillus oryzae</option>
482 <option value="Aspergillus terreus">Aspergillus terreus</option>
483 <option value="Botryotinia fuckeliana">Botryotinia fuckeliana</option>
484 <option value="Cryptococcus neoformans">Cryptococcus neoformans</option>
485 <option value="Fusarium oxysporum">Fusarium oxysporum</option>
486 <option value="Gaeumannomyces graminis">Gaeumannomyces graminis</option>
487 <option value="Gibberella moniliformis">Gibberella moniliformis</option>
488 <option value="Gibberella zeae">Gibberella zeae</option>
489 <option value="Glomerella graminicola">Glomerella graminicola</option>
490 <option value="Komagataella pastoris">Komagataella pastoris</option>
491 <option value="Leptosphaeria maculans">Leptosphaeria maculans</option>
492 <option value="Magnaporthe oryzae">Magnaporthe oryzae</option>
493 <option value="Magnaporthe poae">Magnaporthe poae</option>
494 <option value="Melampsora larici-populina">Melampsora larici-populina</option>
495 <option value="Nectria haematococca">Nectria haematococca</option>
496 <option value="Neosartorya fischeri">Neosartorya fischeri</option>
497 <option value="Neurospora crassa">Neurospora crassa</option>
498 <option value="Phaeosphaeria nodorum">Phaeosphaeria nodorum</option>
499 <option value="Puccinia graminis">Puccinia graminis</option>
500 <option value="Puccinia triticina">Puccinia triticina</option>
501 <option value="Pyrenophora teres">Pyrenophora teres</option>
502 <option value="Pyrenophora tritici-repentis">Pyrenophora tritici-repentis</option>
503 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
504 <option value="Schizosaccharomyces pombe">Schizosaccharomyces pombe</option>
505 <option value="Sclerotinia sclerotiorum">Sclerotinia sclerotiorum</option>
506 <option value="Sporisorium reilianum">Sporisorium reilianum</option>
507 <option value="Trichoderma reesei">Trichoderma reesei</option>
508 <option value="Trichoderma virens">Trichoderma virens</option>
509 <option value="Tuber melanosporum">Tuber melanosporum</option>
510 <option value="Ustilago maydis">Ustilago maydis</option>
511 <option value="Yarrowia lipolytica">Yarrowia lipolytica</option>
512 <option value="Zymoseptoria tritici">Zymoseptoria tritici</option>
513 </param>
514 </when>
515 <when value="Vertebrates">
516 <param name="species" type="select" label="The species to use for the gene annotation"
517 help="">
518 <option value="Ailuropoda melanoleuca">Ailuropoda melanoleuca</option>
519 <option value="Anolis carolinensis">Anolis carolinensis</option>
520 <option value="Bos taurus">Bos taurus</option>
521 <option value="Caenorhabditis elegans">Caenorhabditis elegans</option>
522 <option value="Callithrix jacchus">Callithrix jacchus</option>
523 <option value="Canis familiaris">Canis familiaris</option>
524 <option value="Cavia porcellus">Cavia porcellus</option>
525 <option value="Choloepus hoffmanni">Choloepus hoffmanni</option>
526 <option value="Ciona intestinalis">Ciona intestinalis</option>
527 <option value="Ciona savignyi">Ciona savignyi</option>
528 <option value="Danio rerio">Danio rerio</option>
529 <option value="Dasypus novemcinctus">Dasypus novemcinctus</option>
530 <option value="Dipodomys ordii">Dipodomys ordii</option>
531 <option value="Drosophila melanogaster">Drosophila melanogaster</option>
532 <option value="Echinops telfairi">Echinops telfairi</option>
533 <option value="Equus caballus">Equus caballus</option>
534 <option value="Erinaceus europaeus">Erinaceus europaeus</option>
535 <option value="Felis catus">Felis catus</option>
536 <option value="Gallus gallus">Gallus gallus</option>
537 <option value="Gasterosteus aculeatus">Gasterosteus aculeatus</option>
538 <option value="Gorilla gorilla">Gorilla gorilla</option>
539 <option value="Homo sapiens">Homo sapiens</option>
540 <option value="Ictidomys tridecemlineatus">Ictidomys tridecemlineatus</option>
541 <option value="Latimeria chalumnae">Latimeria chalumnae</option>
542 <option value="Loxodonta africana">Loxodonta africana</option>
543 <option value="Macaca mulatta">Macaca mulatta</option>
544 <option value="Macropus eugenii">Macropus eugenii</option>
545 <option value="Meleagris gallopavo">Meleagris gallopavo</option>
546 <option value="Microcebus murinus">Microcebus murinus</option>
547 <option value="Monodelphis domestica">Monodelphis domestica</option>
548 <option value="Mus musculus">Mus musculus</option>
549 <option value="Mustela putorius furo">Mustela putorius furo</option>
550 <option value="Myotis lucifugus">Myotis lucifugus</option>
551 <option value="Nomascus leucogenys">Nomascus leucogenys</option>
552 <option value="Ochotona princeps">Ochotona princeps</option>
553 <option value="Oreochromis niloticus">Oreochromis niloticus</option>
554 <option value="Ornithorhynchus anatinus">Ornithorhynchus anatinus</option>
555 <option value="Oryctolagus cuniculus">Oryctolagus cuniculus</option>
556 <option value="Oryzias latipes">Oryzias latipes</option>
557 <option value="Otolemur garnettii">Otolemur garnettii</option>
558 <option value="Pan troglodytes">Pan troglodytes</option>
559 <option value="Petromyzon marinus">Petromyzon marinus</option>
560 <option value="Pelodiscus sinensis">Pelodiscus sinensis</option>
561 <option value="Pongo abelii">Pongo abelii</option>
562 <option value="Procavia capensis">Procavia capensis</option>
563 <option value="Pteropus vampyrus">Pteropus vampyrus</option>
564 <option value="Rattus norvegicus">Rattus norvegicus</option>
565 <option value="Saccharomyces cerevisiae">Saccharomyces cerevisiae</option>
566 <option value="Sarcophilus harrisii">Sarcophilus harrisii</option>
567 <option value="Sorex araneus">Sorex araneus</option>
568 <option value="Sus scrofa">Sus scrofa</option>
569 <option value="Taeniopygia guttata">Taeniopygia guttata</option>
570 <option value="Takifugu rubripes">Takifugu rubripes</option>
571 <option value="Tarsius syrichta">Tarsius syrichta</option>
572 <option value="Tetraodon nigroviridis">Tetraodon nigroviridis</option>
573 <option value="Tupaia belangeri">Tupaia belangeri</option>
574 <option value="Tursiops truncatus">Tursiops truncatus</option>
575 <option value="Vicugna pacos">Vicugna pacos</option>
576 <option value="Xenopus tropicalis">Xenopus tropicalis</option>
577 <option value="Xiphophorus maculatus">Xiphophorus maculatus</option>
578 </param>
579 </when>
580 </conditional>
581
582 <param name="missed_cleavages" type="integer" value="2" label="Maximum Missed Cleavages"
583 help="Allow peptides to contain up to this many missed enzyme cleavage sites."/>
584 <param name="fixed_modifications" type="select" label="Fixed Modifications" multiple="true"
585 help="Occurs in known places on peptide sequence. Hold the appropriate key while clicking to select multiple items">
586 <options from_file="searchgui_mods.loc">
587 <column name="name" index="0" />
588 <column name="value" index="0" />
589 </options>
590 </param>
591 <param name="variable_modifications" type="select" label="Variable Modifications" multiple="true"
592 help="Can occur anywhere on the peptide sequence; adds additional error to search score. Hold the appropriate key while clicking to select multiple items">
593 <options from_file="searchgui_mods.loc">
594 <column name="name" index="0" />
595 <column name="value" index="0" />
596 </options>
597 </param>
598 <param name="min_charge" label="Minimum Charge" value="2" type="integer" help="Lowest searched charge value for fragment ions"/>
599 <param name="max_charge" label="Maximum Charge" value="4" type="integer" help="Highest searched charge value for fragment ions"/>
600 <param name="forward_ion" label="Forward Ion" type="select" help="Searched fragment ion type. Select a, b or c based on collisions induced in experiment">
601 <option value="a">a</option>
602 <option value="b" selected="true">b</option>
603 <option value="c">c</option>
604 </param>
605 <param name="reverse_ion" label="Reverse Ion" type="select" help="Searched fragment ion type. Select x, y, or z based on collisions induced in experiment">
606 <option value="x">x</option>
607 <option value="y" selected="true">y</option>
608 <option value="z">z</option>
609 </param>
610 <conditional name="advanced">
611 <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
612 <option value="basic" selected="True">Basic</option>
613 <option value="advanced">Advanced</option>
614 </param>
615 <when value="basic" />
616 <when value="advanced">
617 <conditional name="xtandem">
618 <param name="xtandem_selector" type="select" label="Run X!Tandem search">
619 <option value="yes" selected="True">Search with X!Tandem</option>
620 <option value="no">No X!Tandem search</option>
621 </param>
622 <when value="no" />
623 <when value="yes">
624 <param name="xtandem_npeaks" label="X!Tandem: Total Peaks" type="integer" value="50" help="Maximum number of peaks to be used from a spectrum"/>
625 <param name="xtandem_min_peaks" label="X!Tandem: Min Peaks" type="integer" value="15" help="Minimum number of peaks required for a spectrum to be considered"/>
626 <param name="xtandem_min_frag_mz" label="X!Tandem: Min Frag m/z" type="integer" value="200" help="Fragment mass peaks with m/z less than this value will be discarded"/>
627 <param name="xtandem_min_prec_mass" label="X!Tandem: Min Precursor Mass" type="integer" value="200" help="Minimum mass of 1+ mass of parent ion to be considered"/>
628 <param name="xtandem_noise_suppr" label="X!Tandem: Noise Suppression" type="boolean" checked="true" truevalue="1" falsevalue="0" help="Use noise suppression"/>
629
630 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
631 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
632 <option value="no" selected="True">Don't refine</option>
633 <option value="yes" >Use refinement</option>
634 </param>
635 <when value="no"/>
636 <when value="yes">
637 <param name="xtandem_refine_unc" label="X!Tandem: Unanticipated cleavage, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for unanticipated cleavage during refinement"/>
638 <param name="xtandem_refine_semi" label="X!Tandem: Cleavage semi, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for semi-tryptic peptides during refinement"/>
639 <param name="xtandem_refine_p_mut" label="X!Tandem: Point mutations, refinement" type="boolean" truevalue="1" falsevalue="0" help="Allow for point mutations during refinement"/>
640 <param name="xtandem_refine_snaps" label="X!Tandem: snAPs, refinement" type="boolean" truevalue="1" falsevalue="0" help="Search for known single amino acid polymorphisms during refinement"/>
641 <param name="xtandem_refine_spec_synt" label="X!Tandem: Spectrum synthesis, refinement" type="boolean" truevalue="1" falsevalue="0" help="Use spectrum synthesis scoring"/>
642 </when>
643 </conditional>
644 </when>
645 </conditional>
646
647 <conditional name="omssa">
648 <param name="omssa_selector" type="select" label="Run OMSSA search">
649 <option value="yes" selected="True">Search with OMSSA</option>
650 <option value="no">No OMSSA search</option>
651 </param>
652 <when value="no" />
653 <when value="yes">
654 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
655 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
656 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
657 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
658 </when>
659 </conditional>
660
661 <conditional name="msgf">
662 <param name="msgf_selector" type="select" label="Run MSGF search">
663 <option value="yes" selected="True">Search with MSGF</option>
664 <option value="no">No MSGF search</option>
665 </param>
666 <when value="no" />
667 <when value="yes">
668 <param name="msgf_decoy" label="Search Decoys" type="boolean" truevalue="1" falsevalue="0" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
669 <param name="msgf_min_pep_length" label="Minimum Peptide Length" type="integer" value="6" help="Minimum length for a peptide to be considered"/>
670 <param name="msgf_max_pep_length" label="Maximum Peptide Length" type="integer" value="30" help="Maximum length for a peptide to be considered"/>
671 <param name="msgf_termini" label="Number of tolerable termini" type="select" format="text" help="Searches will take much longer if selecting a value other than 2">
672 <option value="0">0 (ie non-specific cleavage)</option>
673 <option value="1">1 (ie semi-tryptic cleavage)</option>
674 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
675 </param>
676 <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
677 </when>
678 </conditional>
679
680 <conditional name="ms_amanda">
681 <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
682 <option value="yes">Search with MS Amanda</option>
683 <option value="no" selected="True">No MS Amanda search</option>
684 </param>
685 <when value="no" />
686 <when value="yes">
687 </when>
688 </conditional>
689 </when>
690 </conditional>
691 <conditional name="processing_options">
692 <param name="processing_options_selector" type="select" label="Specify Advanced PeptideShaker Processing Options">
693 <option value="no" selected="True">Default Processing Options</option>
694 <option value="yes">Advanced Processing Options</option>
695 </param>
696 <when value="no" />
697 <when value="yes">
698 <param name="protein_fdr" label="FDR at the protein level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
699 <param name="peptide_fdr" label="FDR at the peptide level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
700 <param name="psm_fdr" label="FDR at the PSM level" help="In percent (default 1% FDR: '1')" value="1" type="float" />
701 <param name="protein_fraction_mw_confidence" label="Minimum confidence required for a protein in the fraction MW plot" value="" type="float"
702 help="default 95%: '95.0'" />
703 <conditional name="ptm_score">
704 <param name="ptm_score_selector" type="select" label="The PTM probabilistic score to use for PTM localization">
705 <option value="0" selected="True">A-score</option>
706 <option value="1">PhosphoRS</option>
707 </param>
708 <when value="0" />
709 <when value="1">
710 <param name="score_neutral_losses" label="Include Neutral Losses in A Score" type="boolean" truevalue="1" falsevalue="0" />
711 <param name="ptm_threshold" label="The threshold to use for the PTM scores" value="" type="float"
712 help="Automatic mode will be used if not set" />
713 </when>
714 </conditional>
715 <!-- SKIPPING -protein_fraction_mw_confidence ${processing_options.protein_fraction_mw_confidence} -->
716 </when>
717 </conditional>
718 <conditional name="filtering_options">
719 <param name="filtering_options_selector" type="select" label="Specify Advanced Filtering Options"
720 help="Filter based on peptide lengths, precursor mass error, E value errors from X! Tandem and OMSSA, and include/exclude unknown PTM’s">
721 <option value="no" selected="True">Default Filtering Options</option>
722 <option value="yes">Advanced Processing Options</option>
723 </param>
724 <when value="no" />
725 <when value="yes">
726 <param name="min_peptide_length" label="Minimum Peptide Length" value="6" type="integer" />
727 <param name="max_peptide_length" label="Maximum Peptide Length" value="30" type="integer" />
728 <param name="max_precursor_error" label="Maximum Precursor Error" value="10" type="float" help="Next option specifies units (Da or ppm)" />
729 <param name="max_precursor_error_type" label="Maximum Precursor Error Type" type="select">
730 <option value="0">ppm</option>
731 <option value="1">Daltons</option>
732 </param>
733 <param name="max_xtandem_e" label="Maximum X! Tandem e-value" value="100" type="float" help="" />
734 <param name="max_omssa_e" label="Maximum OMSSA e-value" value="100" type="float" help="" />
735 <param name="max_mascot_e" label="Maximum Mascot e-value filter" value="100" type="float" help="" />
736 <param name="exclude_unknown_ptms" label="Exclude Unknown PTMs" type="boolean" truevalue="1" falsevalue="0" checked="true" />
737 </when>
738 </conditional>
739
740 <param name="outputs" type="select" display="checkboxes" multiple="True" label="Output options">
741 <option value="mzidentML" selected="True">mzidentML File</option>
742 <option value="3" selected="True">Peptide Report</option>
743 <option value="4" selected="True">Protein Report</option>
744 <option value="2">PSM Report</option>
745 <option value="0">Certificate of Analysis</option>
746 <option value="1">Hierarchical Report</option>
747 <option value="cps">CPS file</option>
748 <validator type="no_options" message="Please select at least one output file" />
749 </param>
750 </inputs>
751 <outputs>
752 <data format="mzid" name="mzidentML" from_work_dir="output.mzid" label="${tool.name} on ${on_string}: mzidentML file">
753 <filter>'mzidentML' in outputs</filter>
754 </data>
755 <data format="cps" name="output" from_work_dir="peptide_shaker_output.cps" label="${tool.name} on ${on_string}: CPS file">
756 <filter>'cps' in outputs</filter>
757 </data>
758 <data format="txt" name="output_certificate" from_work_dir="certificate.txt" label="${tool.name} on ${on_string}: Parameters">
759 <filter>'0' in outputs</filter>
760 </data>
761 <data format="tabular" name="output_psm" from_work_dir="psm.txt" label="${tool.name} on ${on_string}: PSM Report">
762 <filter>'2' in outputs</filter>
763 </data>
764 <data format="tabular" name="output_peptides" from_work_dir="peptides.txt" label="${tool.name} on ${on_string}: Peptide Report">
765 <filter>'3' in outputs</filter>
766 </data>
767 <data format="tabular" name="output_proteins" from_work_dir="proteins.txt" label="${tool.name} on ${on_string}: Protein Report">
768 <filter>'4' in outputs</filter>
769 </data>
770 <data format="tabular" name="output_hierarchical" from_work_dir="hierarchical.txt" label="${tool.name} on ${on_string}: Hierarchical Report">
771 <filter>'1' in outputs</filter>
772 </data>
773 </outputs>
774 <tests>
775 <test>
776 <param name="input_database" value="tinydb.fasta"/>
777 <param name="peak_lists" value="tinyspectra.mgf"/>
778 <param name="precursor_ion_tol" value="100"/>
779 <param name="fixed_modifications" value="carbamidomethyl c"/>
780 <param name="variable_modifications" value="oxidation of m"/>
781 <param name="min_charge" value="1"/>
782 <param name="max_charge" value="3"/>
783 <param name="advanced_type_selector" value="advanced"/>
784 <param name="species_type_selector" value="no_species_type"/>
785 <param name="processing_options_selector" value="no"/>
786 <param name="filtering_options_selector" value="no"/>
787 <!--param name="xtandem_selector" value="no"/>-->
788 <param name="xtandem_selector" value="yes"/>
789 <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
790
791 <param name="omssa_selector" value="no"/>
792 <param name="msgf_selector" value="yes"/>
793 <param name="ms_amanda_selector" value="no"/>
794
795 <output name="output" file="tinyoutput.cps" compare="sim_size" delta="600" />
796 </test>
797 </tests>
798 <help>
799 **What it does**
800
801 Runs multiple search engines (X! Tandem, OMSSA and MS-GF+) on any number of MGF peak lists using the SearchGUI application and combines the results.
802
803 https://code.google.com/p/peptide-shaker/
804
805 https://code.google.com/p/searchgui/
806
807 ----
808
809 Reports
810 =======
811
812
813 PSM Report
814 ----------
815
816 * Protein(s): Protein(s) to which the peptide can be attached
817 * Sequence: Sequence of the peptide
818 * Variable Modifications: The variable modifications
819 * D-score: D-score for variable PTM localization
820 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
821 * Localization Confidence: The confidence in variable PTM localization.
822 * Fixed Modifications: The fixed modifications.
823 * Spectrum File: The spectrum file.
824 * Spectrum Title: The title of the spectrum.
825 * Spectrum Scan Number: The spectrum scan number.
826 * RT: Retention time
827 * m/z: Measured m/z
828 * Measured Charge: The charge as given in the spectrum file.
829 * Identification Charge: The charge as inferred by the search engine.
830 * Theoretical Mass: The theoretical mass of the peptide.
831 * Isotope Number: The isotope number targetted by the instrument.
832 * Precursor m/z Error: The precursor m/z matching error.
833 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
834 * Confidence: Confidence in percent associated to the retained PSM.
835 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
836 * Validation: Indicates the validation level of the protein group.
837
838
839 Protein Report
840 --------------
841
842 * Main Accession: Main accession of the protein group.
843 * Description: Description of the protein designed by the main accession.
844 * Gene Name: The gene names of the Ensembl gene ID associated to the main accession.
845 * Chromosome: The chromosome of the Ensembl gene ID associated to the main accession.
846 * PI: Protein Inference status of the protein group.
847 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
848 * Protein Group: The complete protein group (alphabetical order).
849 * #Peptides: Total number of peptides.
850 * #Validated Peptides: Number of validated peptides.
851 * #Unique: Total number of peptides unique to this protein group.
852 * #PSMs: Number of PSMs
853 * #Validated PSMs: Number of validated PSMs
854 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
855 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
856 * MW (kDa): Molecular Weight.
857 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
858 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
859 * Confident Modification Sites: Number of Confident Modification Sites List of the sites where a variable modification was confidently localized.
860 * Other Modification Sites: Number of other Modification Sites List of the non*confident sites where a variable modification was localized.
861 * Score: Score of the protein group.
862 * Confidence: Confidence in percent associated to the protein group.
863 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
864 * Validation: Indicates the validation level of the protein group.
865
866
867 Peptide Report
868 --------------
869
870
871 * Protein(s): Protein(s) to which this peptide can be attached.
872 * AAs Before: The amino-acids before the sequence.
873 * Sequence: Sequence of the peptide.
874 * AAs After: The amino-acids after the sequence.
875 * Modified Sequence: The peptide sequence annotated with variable modifications.
876 * Variable Modifications: The variable modifications.
877 * Localization Confidence: The confidence in PTMs localization.
878 * Fixed Modifications: The fixed modifications.
879 * #Validated PSMs: Number of validated PSMs.
880 * #PSMs: Number of PSMs.
881 * Score: Score of the peptide.
882 * Confidence: Confidence in percent associated to the peptide.
883 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
884 * Validation: Indicates the validation level of the protein group.
885
886
887 Hierachical Report
888 ------------------
889
890 * Main Accession: Main accession of the protein group.
891 * Description: Description of the protein designed by the main accession.
892 * PI: Protein Inference status of the protein group.
893 * Secondary Accessions: Other accessions in the protein group (alphabetical order).
894 * Protein Group: The complete protein group (alphabetical order).
895 * #Peptides: Total number of peptides.
896 * #Validated Peptides: Number of validated peptides.
897 * #Unique: Total number of peptides unique to this protein group.
898 * #PSMs: Number of PSMs
899 * #Validated PSMs: Number of validated PSMs
900 * Coverage (%): Sequence coverage in percent of the protein designed by the main accession.
901 * Possible Coverage (%): Possible sequence coverage in percent of the protein designed by the main accession according to the search settings.
902 * MW (kDa): Molecular Weight.
903 * Spectrum Counting NSAF: Normalized Spectrum Abundance Factor (NSAF)
904 * Spectrum Counting emPAI: exponentially modified Protein Abundance Index (emPAI)
905 * Confident Modification Sites: # Confident Modification Sites List of the sites where a variable modification was confidently localized.
906 * Other Modification Sites: # Other Modification Sites List of the non-confident sites where a variable modification was localized.
907 * Score: Score of the protein group.
908 * Confidence: Confidence in percent associated to the protein group.
909 * Decoy: Indicates whether the protein group is a decoy (1: yes, 0: no).
910 * Validation: Indicates the validation level of the protein group.
911 * Protein(s): Protein(s) to which this peptide can be attached.
912 * AAs Before: The amino-acids before the sequence.
913 * Sequence: Sequence of the peptide.
914 * AAs After: The amino-acids after the sequence.
915 * Variable Modifications: The variable modifications.
916 * Localization Confidence: The confidence in PTMs localization.
917 * Fixed Modifications: The fixed modifications.
918 * #Validated PSMs: Number of validated PSMs.
919 * #PSMs: Number of PSMs.
920 * Score: Score of the peptide.
921 * Confidence: Confidence in percent associated to the peptide.
922 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
923 * Validation: Indicates the validation level of the protein group.
924 * Protein(s): Protein(s) to which the peptide can be attached.
925 * Sequence: Sequence of the peptide.
926 * Modified Sequence: The peptide sequence annotated with variable modifications.
927 * Variable Modifications: The variable modifications.
928 * D-score: D-score for variable PTM localization.
929 * probabilistic PTM score: The probabilistic score (e.g. A-score or PhosphoRS) used for variable PTM localization.
930 * Localization Confidence: The confidence in variable PTM localization.
931 * Fixed Modifications: The fixed modifications.
932 * Spectrum File: The spectrum file.
933 * Spectrum Title: The title of the spectrum.
934 * Spectrum Scan Number: The spectrum scan number.
935 * RT: Retention time
936 * m/z: Measured m/z
937 * Measured Charge: The charge as given in the spectrum file.
938 * Identification Charge: The charge as inferred by the search engine.
939 * Theoretical Mass: The theoretical mass of the peptide.
940 * Isotope Number: The isotope number targetted by the instrument.
941 * Precursor m/z Error: The precursor m/z matching error.
942 * Score: Score of the retained peptide as a combination of the algorithm scores (used to rank PSMs).
943 * Confidence: Confidence in percent associated to the retained PSM.
944 * Decoy: Indicates whether the peptide is a decoy (1: yes, 0: no).
945 * Validation: Indicates the validation level of the protein group.
946
947
948
949
950 ------
951
952 **Citation**
953
954 To cite the underlying tools (PeptideShaker and SearchGUI) please refer to the list of papers at http://peptide-shaker.googlecode.com
955
956 If you use this tool in Galaxy, please cite Chilton J, Ira Cooke, Bjoern Gruening et al. https://bitbucket.org/galaxyp/peptideshaker
957 </help>
958 </tool>