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comparison searchgui.xml @ 21:dfaea053e32f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 327a3944f2f56668d607c3d6cb08ae7d588e208c
author iracooke
date Tue, 16 Jun 2015 23:43:39 -0400
parents 2cafc729b2ae
children e3be595c0bf5
comparison
equal deleted inserted replaced
20:2cafc729b2ae 21:dfaea053e32f
1 <tool id="search_gui" name="Search GUI" version="1.27.0"> 1 <tool id="search_gui" name="Search GUI" version="1.28.0">
2 <description> 2 <description>
3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker 3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
4 </description> 4 </description>
5 <requirements>
6 <requirement type="package" version="1.27">searchgui</requirement>
7 </requirements>
8 <macros> 5 <macros>
9 <import>macros.xml</import> 6 <import>macros.xml</import>
10 </macros> 7 </macros>
8 <requirements>
9 <requirement type="package" version="1.28">searchgui</requirement>
10 <environment_variable name="LC_ALL" action="set_to">C</environment_variable>
11 </requirements>
11 <expand macro="stdio" /> 12 <expand macro="stdio" />
12 <command> 13 <command>
13 <![CDATA[ 14 <![CDATA[
14 #from datetime import datetime 15 #from datetime import datetime
15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
32 #if $create_decoy: 33 #if $create_decoy:
33 echo "Creating decoy database."; 34 echo "Creating decoy database.";
34 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && 35 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
35 rm input_database.fasta && 36 rm input_database.fasta &&
36 cp input_database_concatenated_target_decoy.fasta input_database.fasta && 37 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
37 ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; 38 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
38 #end if 39 #end if
39 40
40 ##################################################### 41 #####################################################
41 ## generate IdentificationParameters for SearchGUI ## 42 ## generate IdentificationParameters for SearchGUI ##
42 ##################################################### 43 #####################################################
46 47
47 @GENERAL_PARAMETERS@ 48 @GENERAL_PARAMETERS@
48 49
49 -db input_database.fasta 50 -db input_database.fasta
50 51
51 #if $advanced.advanced_type_selector == "advanced": 52 #if $xtandem.xtandem_advanced == "yes"
52 53
53 #if $advanced.xtandem.xtandem_selector == "yes" 54 -xtandem_npeaks ${xtandem.xtandem_npeaks}
54 55 -xtandem_min_peaks ${xtandem.xtandem_min_peaks}
55 -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks} 56 -xtandem_min_frag_mz ${xtandem.xtandem_min_frag_mz}
56 -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks} 57 -xtandem_min_prec_mass ${xtandem.xtandem_min_prec_mass}
57 -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz} 58 -xtandem_noise_suppr ${xtandem.xtandem_noise_suppr}
58 -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass} 59 -xtandem_dynamic_range ${xtandem.xtandem_dynamic_range}
59 -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr} 60 -xtandem_quick_acetyl ${xtandem.xtandem_quick_acetyl}
60 61 -xtandem_quick_pyro ${xtandem.xtandem_quick_pyro}
61 #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes" 62 -xtandem_stp_bias ${xtandem.xtandem_stp_bias}
62 -xtandem_refine 1 63 -xtandem_evalue ${xtandem.xtandem_evalue}
63 -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc} 64 -xtandem_output_proteins ${xtandem.xtandem_output_proteins}
64 -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi} 65 -xtandem_output_sequences ${xtandem.xtandem_output_sequences}
65 -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut} 66 -xtandem_output_spectra ${xtandem.xtandem_output_spectra}
66 -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps} 67 ## -xtandem_skyline_path ${xtandem.xtandem_skyline_path}
67 -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt} 68
68 #end if 69 #if $xtandem.xtandem_refine.xtandem_refine_selector == "yes"
70 -xtandem_refine 1
71 -xtandem_refine_unc ${xtandem.xtandem_refine.xtandem_refine_unc}
72 -xtandem_refine_semi ${xtandem.xtandem_refine.xtandem_refine_semi}
73 -xtandem_refine_p_mut ${xtandem.xtandem_refine.xtandem_refine_p_mut}
74 -xtandem_refine_snaps ${xtandem.xtandem_refine.xtandem_refine_snaps}
75 -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt}
76 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot}
77 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
78
69 #end if 79 #end if
70 80 #end if
71 #if $advanced.omssa.omssa_selector == "yes" 81
72 -omssa_hitlist_length ${advanced.omssa.hitlist_length} 82 #if $omssa.omssa_advanced == "yes"
73 -omssa_remove_prec ${advanced.omssa.remove_precursor} 83 -omssa_hitlist_length ${omssa.hitlist_length}
74 -omssa_scale_prec ${advanced.omssa.scale_precursor} 84 -omssa_remove_prec ${omssa.remove_precursor}
75 -omssa_estimate_charge ${advanced.omssa.estimate_charge} 85 -omssa_scale_prec ${omssa.scale_precursor}
86 -omssa_estimate_charge ${omssa.estimate_charge}
87
88 -omssa_memory ${omssa.omssa_memory}
89 -omssa_isotopes ${omssa.omssa_isotopes}
90 -omssa_neutron ${omssa.omssa_neutron}
91 -omssa_low_intensity "${omssa.omssa_low_intensity}"
92 -omssa_high_intensity ${omssa.omssa_high_intensity}
93 -omssa_intensity_incr ${omssa.omssa_intensity_incr}
94 -omssa_single_window_wd ${omssa.omssa_single_window_wd}
95 -omssa_double_window_wd ${omssa.omssa_double_window_wd}
96 -omssa_single_window_pk ${omssa.omssa_single_window_pk}
97 -omssa_double_window_pk ${omssa.omssa_double_window_pk}
98 -omssa_min_ann_int_pks ${omssa.omssa_min_ann_int_pks}
99 -omssa_min_annotated_peaks ${omssa.omssa_min_annotated_peaks}
100 -omssa_min_peaks ${omssa.omssa_min_peaks}
101 -omssa_methionine ${omssa.omssa_methionine}
102 -omssa_max_ladders ${omssa.omssa_max_ladders}
103 -omssa_max_frag_charge ${omssa.omssa_max_frag_charge}
104 -omssa_fraction ${omssa.omssa_fraction}
105 -omssa_plus_one ${omssa.omssa_plus_one}
106 -omssa_charge ${omssa.omssa_charge}
107 -omssa_prec_per_spectrum ${omssa.omssa_prec_per_spectrum}
108 -omssa_forward ${omssa.omssa_forward}
109 -omssa_rewind ${omssa.omssa_rewind}
110 -omssa_max_frag_series ${omssa.omssa_max_frag_series}
111 -omssa_corr ${omssa.omssa_corr}
112 -omssa_consecutive_p ${omssa.omssa_consecutive_p}
113 -omssa_it_sequence_evalue ${omssa.omssa_it_sequence_evalue}
114 -omssa_it_spectrum_evalue ${omssa.omssa_it_spectrum_evalue}
115 -omssa_it_replace_evalue ${omssa.omssa_it_replace_evalue}
116 -omssa_max_evalue ${omssa.omssa_max_evalue}
117 -omssa_hitlist_charge ${omssa.omssa_hitlist_charge}
118 -omssa_min_pep_length ${omssa.omssa_min_pep_length}
119 -omssa_max_pep_length ${omssa.omssa_max_pep_length}
120 -omssa_format ${omssa.omssa_format}
121 #end if
122
123 #if $msgf.msgf_advanced == "yes"
124 -msgf_decoy ${msgf.msgf_decoy}
125 -msgf_min_pep_length ${msgf.msgf_min_pep_length}
126 -msgf_max_pep_length ${msgf.msgf_max_pep_length}
127 -msgf_termini ${msgf.msgf_termini}
128 -msgf_num_ptms ${msgf.msgf_num_ptms}
129 -msgf_instrument ${msgf.msgf_instrument}
130 -msgf_fragmentation ${msgf.msgf_fragmentation}
131 -msgf_protocol ${msgf.msgf_protocol}
132 -msgf_num_matches ${msgf.msgf_num_matches}
133 -msgf_additional ${msgf.msgf_additional}
134 -msgf_isotope_low ${msgf.msgf_isotope_low}
135 -msgf_isotope_high ${msgf.msgf_isotope_high}
136 #end if
137
138 #if $ms_amanda.ms_amanda_advanced == "yes"
139 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
140 -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
141 -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument}
142 -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank}
143 -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
144 #end if
145
146 #if $myrimatch.myrimatch_advanced == "yes"
147 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
148 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
149 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
150 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
151 -myrimatch_isotope_low ${myrimatch.myrimatch_isotope_low}
152 -myrimatch_isotope_high ${myrimatch.myrimatch_isotope_high}
153 -myrimatch_num_matches ${myrimatch.myrimatch_num_matches}
154 -myrimatch_num_ptms ${myrimatch.myrimatch_num_ptms}
155 -myrimatch_fragmentation ${myrimatch.myrimatch_fragmentation}
156 -myrimatch_termini ${myrimatch.myrimatch_termini}
157 -myrimatch_plus_three ${myrimatch.myrimatch_plus_three}
158 -myrimatch_xcorr ${myrimatch.myrimatch_xcorr}
159 -myrimatch_tic_cutoff ${myrimatch.myrimatch_tic_cutoff}
160 -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes}
161 -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier}
162 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
163 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}
164 #end if
165
166 #if $tide.tide_advanced == "yes"
167 -tide_num_ptms ${tide.tide_num_ptms}
168 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
169 -tide_min_pep_length ${tide.tide_min_pep_length}
170 -tide_max_pep_length ${tide.tide_max_pep_length}
171 -tide_min_prec_mass ${tide.tide_min_prec_mass}
172 -tide_max_prec_mass ${tide.tide_max_prec_mass}
173 -tide_decoy_format ${tide.tide_decoy_format}
174 -tide_keep_terminals ${tide.tide_keep_terminals}
175
176 -tide_output_folder ${tide.tide_output_folder}
177 -tide_print_peptides ${tide.tide_print_peptides}
178 -tide_verbosity ${tide.tide_verbosity}
179 -tide_monoisotopic ${tide.tide_monoisotopic}
180 -tide_clip_n_term ${tide.tide_clip_n_term}
181 -tide_digestion_type ${tide.tide_digestion_type}
182 -tide_compute_sp ${tide.tide_compute_sp}
183 -tide_max_psms ${tide.tide_max_psms}
184 -tide_compute_p ${tide.tide_compute_p}
185 -tide_min_spectrum_mz ${tide.tide_min_spectrum_mz}
186 -tide_max_spectrum_mz ${tide.tide_max_spectrum_mz}
187 -tide_min_spectrum_peaks ${tide.tide_min_spectrum_peaks}
188 -tide_spectrum_charges ${tide.tide_spectrum_charges}
189 -tide_remove_prec ${tide.tide_remove_prec}
190 -tide_remove_prec_tol ${tide.tide_remove_prec_tol}
191 -tide_progress_indicator ${tide.tide_progress_indicator}
192 -tide_use_flanking ${tide.tide_use_flanking}
193 -tide_use_neutral_losses ${tide.tide_use_neutral_losses}
194 -tide_mz_bin_width ${tide.tide_mz_bin_width}
195 -tide_mz_bin_offset ${tide.tide_mz_bin_offset}
196 -tide_concat ${tide.tide_concat}
197 -tide_export_text ${tide.tide_export_text}
198 -tide_export_sqt ${tide.tide_export_sqt}
199 -tide_export_pepxml ${tide.tide_export_pepxml}
200 -tide_export_mzid ${tide.tide_export_mzid}
201 -tide_export_pin ${tide.tide_export_pin}
202 -tide_remove_temp ${tide.tide_remove_temp}
203 #end if
204
205 #if $comet.comet_advanced == "yes"
206
207 #if $comet.comet_spectrum.comet_spectrum_selector == "yes"
208 -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
209 -comet_min_peak_int ${comet.comet_spectrum.comet_min_peak_int}
210 -comet_remove_prec ${comet.comet_spectrum.comet_remove_prec}
211
212
213 #if $comet.comet_spectrum.comet_remove_prec == "1"
214 -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
215 #end if
216
217 #if $comet.comet_spectrum.comet_remove_prec == "2"
218 -comet_remove_prec_tol ${comet.comet_spectrum.comet_remove_prec_tol}
219 #end if
220
221 -comet_clear_mz_range_lower ${comet.comet_spectrum.comet_clear_mz_range_lower}
222 -comet_clear_mz_range_upper ${comet.comet_spectrum.comet_clear_mz_range_upper}
76 #end if 223 #end if
77 224
78 #if $advanced.msgf.msgf_selector == "yes" 225 #if $comet.comet_search.comet_search_selector == "yes"
79 -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length} 226 -comet_enzyme_type ${comet.comet_search.comet_enzyme_type}
80 -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length} 227 -comet_isotope_correction ${comet.comet_search.comet_isotope_correction}
81 -msgf_termini ${advanced.msgf.msgf_termini} 228 -comet_min_prec_mass ${comet.comet_search.comet_min_prec_mass}
82 -msgf_num_ptms ${advanced.msgf.msgf_num_ptms} 229 -comet_max_prec_mass ${comet.comet_search.comet_max_prec_mass}
230 -comet_num_matches ${comet.comet_search.comet_num_matches}
231 -comet_max_frag_charge ${comet.comet_search.comet_max_frag_charge}
232 -comet_remove_meth ${comet.comet_search.comet_remove_meth}
233 -comet_batch_size ${comet.comet_search.comet_batch_size}
234 -comet_num_ptms ${comet.comet_search.comet_num_ptms}
83 #end if 235 #end if
84 236
85 ##if $advanced.ms_amanda.ms_amanda_selector == "yes" 237 #if $comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
86 ##end if 238 -comet_frag_bin_offset ${comet.comet_fragment_ions.comet_frag_bin_offset}
87 239 -comet_sparse_matrix ${comet.comet_fragment_ions.comet_sparse_matrix}
240 -comet_theoretical_fragment_ions ${comet.comet_fragment_ions.comet_theoretical_fragment_ions}
241 #end if
88 #end if 242 #end if
89 243
90 2> $temp_stderr) 244 2> $temp_stderr)
91 && 245 &&
92 246
98 -spectrum_files \$cwd 252 -spectrum_files \$cwd
99 -output_folder \$cwd/output 253 -output_folder \$cwd/output
100 -id_params SEARCHGUI_IdentificationParameters.parameters 254 -id_params SEARCHGUI_IdentificationParameters.parameters
101 255
102 -threads "\${GALAXY_SLOTS:-12}" 256 -threads "\${GALAXY_SLOTS:-12}"
103 -correct_titles "${correct_titles}" 257
104 $missing_titles 258 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
105 -mgf_splitting "${mgf_splitting}" 259 -correct_titles "${searchgui_advanced.correct_titles}"
106 -mgf_spectrum_count "${mgf_spectrum_count}" 260 $searchgui_advanced.missing_titles
261 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
262 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
263 #end if
107 264
108 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created 265 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
109 ## the tree is generated afterwards in PeptideShaker 266 ## the tree is generated afterwards in PeptideShaker
110 -protein_index 0 267 -protein_index 0
111 268
112 ##-makeblastdb_folder \$BLAST_ROOT_DIR 269 ##-makeblastdb_folder \$BLAST_ROOT_DIR
113 270
114 #if $advanced.advanced_type_selector == "advanced": 271 #set $engines_list = str($engines).split(',')
115 272 #if 'X!Tandem' in $engines_list:
116 #if $advanced.xtandem.xtandem_selector == "yes" 273 -xtandem 1
117 -xtandem 1
118 #else
119 -xtandem 0
120 #end if
121
122 #if $advanced.omssa.omssa_selector == "yes"
123 -omssa 1
124 #else
125 -omssa 0
126 #end if
127
128 #if $advanced.msgf.msgf_selector == "yes"
129 -msgf 1
130 #else
131 -msgf 0
132 #end if
133
134 #if $advanced.myrimatch.myrimatch_selector == "yes"
135 -myrimatch 1
136 #else
137 -myrimatch 0
138 #end if
139
140 #if $advanced.comet.comet_selector == "yes"
141 -comet 1
142 #else
143 -comet 0
144 #end if
145
146 #if $advanced.ms_amanda.ms_amanda_selector == "yes"
147 -ms_amanda 1
148 #else
149 -ms_amanda 0
150 #end if
151
152 #if $advanced.tide.tide_selector == "yes"
153 -tide 1
154 #else
155 -tide 0
156 #end if
157
158 #else 274 #else
159 -ms_amanda 0 -tide 0 275 -xtandem 0
160 #end if 276 #end if
161 277
278 #if 'MyriMatch' in $engines_list:
279 -myrimatch 1
280 #else
281 -myrimatch 0
282 #end if
283
284 #if 'MSGF' in $engines_list:
285 -msgf 1
286 #else
287 -msgf 0
288 #end if
289
290 #if 'OMSSA' in $engines_list:
291 -omssa 1
292 #else
293 -omssa 0
294 #end if
295
296 #if 'Comet' in $engines_list:
297 -comet 1
298 #else
299 -comet 0
300 #end if
301
302 #if 'Tide' in $engines_list:
303 -tide 1
304 #else
305 -tide 0
306 #end if
307
308 #if 'MS_Amanda' in $engines_list:
309 -ms_amanda 1
310 #else
311 -ms_amanda 0
312 #end if
313
162 ## single zip file 314 ## single zip file
163 -output_option 0 315 -output_option 0
164 316
165 ## mgf and database in output 317 ## mgf and database in output
166 -output_data 1 318 -output_data 1
177 cat $temp_stderr 2>&1; 329 cat $temp_stderr 2>&1;
178 (exit \$exit_code_for_galaxy) 330 (exit \$exit_code_for_galaxy)
179 ]]> 331 ]]>
180 </command> 332 </command>
181 <inputs> 333 <inputs>
334
182 <param format="fasta" name="input_database" type="data" label="Protein Database" 335 <param format="fasta" name="input_database" type="data" label="Protein Database"
183 help="Select FASTA database from history"/> 336 help="Select FASTA database from history"/>
184 337
185 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" 338 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
186 label="Create a concatenated target/decoy database before running PeptideShaker" 339 label="Create a concatenated target/decoy database before running PeptideShaker"
187 help="Selecting this option will help PeptideShaker calculate FDR values" /> 340 help="Selecting this option will help PeptideShaker calculate FDR values" />
188 341
189 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" 342 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
190 help="Select appropriate MGF dataset(s) from history" /> 343 help="Select appropriate MGF dataset(s) from history" />
191 344
345 <!-- Search Engine Selection -->
346 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
347 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
348 <option value="X!Tandem" selected="True">X!Tandem</option>
349 <option value="MyriMatch">MyriMatch</option>
350 <option value="MS_Amanda">MS_Amanda</option>
351 <option value="MSGF" selected="True">MS-GF+</option>
352 <option value="OMSSA" selected="True">OMSSA</option>
353 <option value="Comet">Comet</option>
354 <option value="Tide">Tide</option>
355 <validator type="no_options" message="Please select at least one output file" />
356 </param>
357
358
359 <!-- General Parameters -->
192 <expand macro="general_options"/> 360 <expand macro="general_options"/>
193 361
194 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" 362 <!-- Optional Advanced SearchGUI Parameters -->
195 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> 363 <conditional name="searchgui_advanced">
196 <option value="0">no correction</option> 364 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
197 <option value="1" selected="True">rename spectra</option> 365 <option value="basic" selected="True">Default</option>
198 <option value="2">delete spectra</option>
199 </param>
200
201 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
202 label="Add missing spectrum titles" help="(-missing_titles)"/>
203
204 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
205 help="Choose a smaller value if you are running on a machine with limited memory"/>
206
207 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
208 help="Choose a smaller value if you are running on a machine with limited memory"/>
209
210 <conditional name="advanced">
211 <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
212 <option value="basic" selected="True">Basic</option>
213 <option value="advanced">Advanced</option> 366 <option value="advanced">Advanced</option>
214 </param> 367 </param>
215 <when value="basic" /> 368 <when value="basic" />
216 <when value="advanced"> 369 <when value="advanced">
217 <conditional name="xtandem"> 370 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
218 <param name="xtandem_selector" type="select" label="Run X!Tandem search"> 371 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
219 <option value="yes" selected="True">Search with X!Tandem</option> 372 <option value="0">no correction</option>
220 <option value="no">No X!Tandem search</option> 373 <option value="1" selected="True">rename spectra</option>
374 <option value="2">delete spectra</option>
375 </param>
376
377 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
378 label="Add missing spectrum titles" help="(-missing_titles)"/>
379
380 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
381 help="Choose a smaller value if you are running on a machine with limited memory"/>
382
383 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
384 help="Choose a smaller value if you are running on a machine with limited memory"/>
385 </when>
386 </conditional>
387
388
389 <!-- X!TANDEM ADVANCED PARAMETERS -->
390 <conditional name="xtandem">
391 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
392 <option value="yes">Advanced</option>
393 <option value="no" selected="True">Default</option>
394 </param>
395 <when value="no" />
396 <when value="yes">
397 <param name="xtandem_npeaks" type="integer" value="50"
398 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
399 <param name="xtandem_min_peaks" type="integer" value="15"
400 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
401 <param name="xtandem_min_frag_mz" type="integer" value="200"
402 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
403 <param name="xtandem_min_prec_mass" type="integer" value="200"
404 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
405 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
406 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
407 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
408 label="X!Tandem: Dynamic Range" value="100" type="integer" />
409 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
410 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
411 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
412 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
413 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
414 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
415 <param name="xtandem_evalue" help="Highest value for recorded peptides"
416 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="100" />
417 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
418 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
419 <param name="xtandem_output_sequences" help="Controls output of sequence information"
420 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
421 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
422 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" />
423 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
424
425 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
426 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
427 <option value="no" selected="True">Don't refine</option>
428 <option value="yes" >Use refinement</option>
429 </param>
430 <when value="no"/>
431 <when value="yes">
432 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
433 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
434 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
435 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
436 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
437 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
438 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
439 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
440 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
441 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
442 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
443 label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
444 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
445 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
446 </when>
447 </conditional>
448 </when>
449 </conditional>
450
451 <!-- OMSSA ADVANCED PARAMETERS -->
452 <conditional name="omssa">
453 <param name="omssa_advanced" type="select" label="OMSSA Options">
454 <option value="yes">Advanced</option>
455 <option value="no" selected="True">Default</option>
456 </param>
457 <when value="no" />
458 <when value="yes">
459 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
460 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
461 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
462 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
463
464 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
465 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
466 <!-- param name="omssa_isotopes" type="integer" value="0"
467 label="OMSSA: Number of Isotopes" help="Number of isotopes to use (integer), 0 implies monoisotopic (default)" / -->
468 <param name="omssa_neutron" type="float" value="1446.94"
469 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
470 <param name="omssa_low_intensity" type="float" value="0.0"
471 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
472 <param name="omssa_high_intensity" type="float" value="0.2"
473 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
474 <param name="omssa_intensity_incr" type="float" value="0.0005"
475 label="OMSSA: Intensity Increment" help="Intensity increment" />
476 <param name="omssa_single_window_wd" type="integer" value="27"
477 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
478 <param name="omssa_double_window_wd" type="integer" value="14"
479 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
480 <param name="omssa_single_window_pk" type="integer" value="2"
481 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
482 <param name="omssa_double_window_pk" type="integer" value="2"
483 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
484 <param name="omssa_min_ann_int_pks" type="integer" value="6"
485 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
486 <param name="omssa_min_annotated_peaks" type="integer" value="2"
487 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
488 <param name="omssa_min_peaks" type="integer" value="4"
489 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
490 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
491 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
492 <param name="omssa_max_ladders" type="integer" value="128"
493 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
494 <param name="omssa_max_frag_charge" type="integer" value="2"
495 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
496 <param name="omssa_fraction" type="float" value="0.95"
497 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
498 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
499 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
500 <param name="omssa_charge" type="select"
501 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
502 <option value="0" >Minus</option>
503 <option value="1" selected="True">Plus</option>
504 </param>
505 <param name="omssa_prec_per_spectrum" type="integer" value="1"
506 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
507 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
508 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
509 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
510 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
511 <param name="omssa_max_frag_series" type="integer" value="100"
512 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
513 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
514 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
515 <param name="omssa_consecutive_p" type="float" value="0.5"
516 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
517 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
518 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
519 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
520 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
521 <param name="omssa_it_replace_evalue" type="float" value="0.01"
522 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
523 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
524 label="OMSSA: Remove Precursor" help="Remove precursors" />
525 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
526 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
527 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
528 label="OMSSA: Remove Precursor" help="Remove precursors" />
529 <param name="omssa_max_evalue" type="float" value="100"
530 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
531 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
532 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
533 <param name="omssa_it_replace_evalue" type="float" value="100"
534 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
535 <param name="omssa_hitlist_length" type="integer" value="0"
536 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
537 <param name="omssa_hitlist_charge" type="integer" value="30"
538 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
539 <param name="omssa_min_pep_length" type="integer" value="4"
540 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
541 <param name="omssa_max_pep_length" type="integer" value="40"
542 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
543 <param name="omssa_format" label="OMSSA output format" type="select" >
544 <option value="0" selected="True">OMX</option>
545 <option value="1" >CSV</option>
546 </param>
547 </when>
548 </conditional>
549
550 <!-- MS-GF+ ADVANCED PARAMETERS -->
551 <conditional name="msgf">
552 <param name="msgf_advanced" type="select" label="MSGF Options">
553 <option value="yes">Advanced</option>
554 <option value="no" selected="True">Default</option>
555 </param>
556 <when value="no" />
557 <when value="yes">
558 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
559 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
560 <param name="msgf_min_pep_length" type="integer" value="6"
561 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
562 <param name="msgf_max_pep_length" type="integer" value="30"
563 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
564 <param name="msgf_termini" type="select" format="text"
565 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
566 <option value="0">0 (ie non-specific cleavage)</option>
567 <option value="1">1 (ie semi-tryptic cleavage)</option>
568 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
569 </param>
570 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
571
572 <param name="msgf_instrument" label="MSGF: Instrument type" type="select" help="Identifier of the instrument to generate MS/MS spectra (used to determine the scoring model)">
573 <option value="0" selected="True">Low-res LCQ/LTQ</option>
574 <option value="1" >High-res LTQ</option>
575 <option value="2" >TOF</option>
576 <option value="3" >Q-Exactive</option>
577 </param>
578 <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
579 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
580 <option value="1" >CID</option>
581 <option value="2" >ETD</option>
582 <option value="3" >HCD</option>
583 </param>
584 <param name="msgf_protocol" label="MSGF: Protocol type" type="select" help="Protocol identifier. Protocols are used to enable scoring parameters for enriched and/or labeled samples">
585 <option value="0" selected="True">Automatic</option>
586 <option value="1" >Phosphorylation</option>
587 <option value="2" >iTRAQ</option>
588 <option value="3" >iTRAQPhospho</option>
589 <option value="4" >TMT</option>
590 <option value="5" >Standard</option>
591 </param>
592 <param name="msgf_num_matches" label="MSGF: Maximum Number of Spectrum Matches" type="integer" value="1" help="Number of peptide matches per spectrum to report" />
593 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
594 <option value="0" selected="True">output basic scores only</option>
595 <option value="1" >output additional features</option>
596 </param>
597 <param name="msgf_isotope_low" label="MSGF: Lower Isotope Error Range" type="integer" value="0" help="Lower isotope error range" />
598 <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" />
599 </when>
600 </conditional>
601
602 <!-- MS-AMANDA ADVANCED PARAMETERS -->
603 <conditional name="ms_amanda">
604 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
605 <option value="yes">Advanced</option>
606 <option value="no" selected="True">Default</option>
607 </param>
608 <when value="no" />
609 <when value="yes">
610 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
611 label="MS Amanda: Generate Decoys" help="generate decoys" />
612 <param name="ms_amanda_max_evalue" type="float" value="100"
613 label="MS Amanda: Maximal Evalue" help="MS Amanda maximal evalue considered" />
614 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="float" value="100" help="MS Amanda instrument id option. Available enzymes are listed in the GUI. (Note: case sensitive.)." />
615 <param name="ms_amanda_max_rank" type="integer" value="5"
616 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
617 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
618 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
619 </when>
620 </conditional>
621
622
623 <!-- TIDE ADVANCED PARAMETERS -->
624 <conditional name="tide">
625 <param name="tide_advanced" type="select" label="TIDE Options">
626 <option value="yes">Advanced</option>
627 <option value="no" selected="True">Default</option>
628 </param>
629 <when value="no" />
630 <when value="yes">
631 <param name="tide_num_ptms" type="integer" value="100"
632 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
633 <param name="tide_num_ptms_per_type" type="integer" value="2"
634 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
635 <param name="tide_min_pep_length" type="integer" value="6"
636 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
637 <param name="tide_max_pep_length" type="integer" value="30"
638 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
639 <param name="tide_min_prec_mass" type="float" value="200.0"
640 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
641 <param name="tide_max_prec_mass" type="float" value="7200.0"
642 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
643 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
644 <option value="none" selected="True">none</option>
645 <option value="shuffle" >shuffle</option>
646 <option value="peptide-revers" >peptide-reverse</option>
647 <option value="protein-reverse" >protein-reverse</option>
648 </param>
649 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
650 <option value="N" >N</option>
651 <option value="C" >C</option>
652 <option value="NC" selected="True">NC</option>
653 <option value="non" >none</option>
654 </param>
655 <param name="tide_decoy_seed" type="integer" value="1"
656 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
657 <param name="tide_output_folder" type="text" value="crux-output"
658 label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/>
659 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
660 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
661 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
662 <option value="0" >0</option>
663 <option value="10" >10</option>
664 <option value="20" >20</option>
665 <option value="30" selected="True">30</option>
666 <option value="40" >40</option>
667 <option value="50" >50</option>
668 <option value="60" >60</option>
669 </param>
670
671 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
672 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
673 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
674 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
675 <param name="tide_digestion_type" label="TIDE: Digestion Type" type="select" help="Either both ends (full-digest) or at least one end (partial-digest) of a peptide must conform to enzyme specificity rules">
676 <option value="full-digest" selected="True">full-digest</option>
677 <option value="partial-digest" >partial-digest</option>
678 </param>
679 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
680 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
681 <param name="tide_max_psms" type="integer" value="10"
682 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
683 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
684 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
685 <param name="tide_min_spectrum_mz" type="float" value="0.0"
686 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
687 <param name="tide_max_spectrum_mz" type="float" value="100000.0"
688 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
689 <param name="tide_min_spectrum_peaks" type="integer" value="20"
690 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
691 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
692 <option value="1" >1</option>
693 <option value="2" >2</option>
694 <option value="3" >3</option>
695 <option value="all" selected="True">all</option>
696 </param>
697 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
698 label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
699 <param name="tide_remove_prec_tol" type="float" value="1.5"
700 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
701 <param name="tide_progress_indicator" type="integer" value="1000"
702 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
703 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
704 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
705 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
706 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
707 <param name="tide_mz_bin_width" type="float" value="0.02"
708 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
709 <param name="tide_mz_bin_offset" type="float" value="0.0"
710 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
711 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
712 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
713 <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true"
714 label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/>
715 <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false"
716 label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/>
717 <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false"
718 label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/>
719 <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false"
720 label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/>
721 <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false"
722 label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
723 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
724 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
725 </when>
726 </conditional>
727
728 <!-- MyriMatch ADVANCED PARAMETERS -->
729 <conditional name="myrimatch">
730 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
731 <option value="yes">Advanced</option>
732 <option value="no" selected="True">Default</option>
733 </param>
734 <when value="no" />
735 <when value="yes">
736 <param name="myrimatch_min_pep_length" type="integer" value="6"
737 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
738 <param name="myrimatch_max_pep_length" type="integer" value="30"
739 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
740 <param name="myrimatch_min_prec_mass" type="float" value="0.0"
741 label="MyriMatch: Minimum Peptide Mass" help="Minimum 1+ mass of parent ion to be considered" />
742 <param name="myrimatch_max_prec_mass" type="float" value="10000.0"
743 label="MyriMatch: Maximum Peptide Mass" help="Maximum 1+ mass of parent ion to be considered" />
744 <param name="myrimatch_isotope_low" type="integer" value="-1"
745 label="MyriMatch: Lower Isotope Error Range" help="Lower isotope error ragne" />
746 <param name="myrimatch_isotope_high" type="integer" value="2"
747 label="MyriMatch: Upper Isotope Error Range" help="Upper isotope error range" />
748 <param name="myrimatch_num_matches" type="integer" value="10"
749 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
750 <param name="myrimatch_num_ptms" type="integer" value="2"
751 label="MyriMatch: Number of PTMs" help="Set the number of PTMS allowed per peptide" />
752 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
753 <option value="CID" selected="True">CID</option>
754 <option value="ETD" >ETD</option>
755 </param>
756 <param name="myrimatch_termini" label="MyriMatch: Number of Enzymatic Termini" type="select" help="Select the number of enzymatic termini">
757 <option value="0">non-tryptic</option>
758 <option value="1" >semi-tryptic</option>
759 <option value="2" selected="True" >fully-tryptic</option>
760 </param>
761 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
762 label="MyriMatch: Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
763 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
764 label="MyriMatch: Xcorr Option" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
765 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
766 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained" />
767 <param name="myrimatch_intensity_classes" type="integer" value="3"
768 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
769 <param name="myrimatch_class_multiplier" type="integer" value="2"
770 label="MyriMatch: Class Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
771 <param name="myrimatch_num_batches" type="integer" value="50"
772 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
773 <param name="myrimatch_max_peak" type="integer" value="100"
774 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
775 </when>
776 </conditional>
777
778 <!-- Comet ADVANCED PARAMETERS -->
779 <conditional name="comet">
780 <param name="comet_advanced" type="select" label="Comet Options">
781 <option value="yes">Advanced</option>
782 <option value="no" selected="True">Default</option>
783 </param>
784 <when value="no" />
785 <when value="yes">
786 <!-- Spectrum Related parameters -->
787 <conditional name="comet_spectrum">
788 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
789 <option value="yes">Set Spectrum Parameters</option>
790 <option value="no" selected="True">Keep Default Spectrum Parameters</option>
221 </param> 791 </param>
222 <when value="no" /> 792 <when value="no" />
223 <when value="yes"> 793 <when value="yes">
224 <param name="xtandem_npeaks" type="integer" value="50" 794 <param name="comet_min_peaks" type="integer" value="10"
225 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/> 795 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
226 <param name="xtandem_min_peaks" type="integer" value="15" 796 <param name="comet_min_peak_int" type="float" value="0.0"
227 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/> 797 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
228 <param name="xtandem_min_frag_mz" type="integer" value="200" 798 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
229 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/> 799 <option value="0" selected="True" >off</option>
230 <param name="xtandem_min_prec_mass" type="integer" value="200" 800 <option value="1">on</option>
231 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/> 801 <option value="2">as expected for ETD/ECD spectra</option>
232 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0" 802 </param>
233 label="X!Tandem: Noise Suppression" help="Use noise suppression"/> 803 <when value="0" />
234 804 <when value="1">
235 <conditional name="xtandem_refine"><!-- -xtandem_refine --> 805 <param name="comet_remove_prec_tol" type="float" value="1.5"
236 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> 806 label="Comet: Remove Precursor Tolerance" />
237 <option value="no" selected="True">Don't refine</option> 807 </when>
238 <option value="yes" >Use refinement</option> 808 <when value="2">
239 </param> 809 <param name="comet_remove_prec_tol" type="float" value="1.5"
240 <when value="no"/> 810 label="Comet: Remove Precursor Tolerance" />
241 <when value="yes"> 811 </when>
242 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" 812 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
243 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/> 813 label="Comet: Minimum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, lower m/z range" />
244 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" 814 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
245 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/> 815 label="Comet: Maximum Peaks Intensity" help="Intended for iTRAQ/TMT type data where one might want to remove the reporter ion signals, upper m/z range" />
246 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0"
247 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
248 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0"
249 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
250 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0"
251 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
252 </when>
253 </conditional>
254 </when> 816 </when>
255 </conditional> 817 </conditional>
256 818 <!-- Search Related parameters -->
257 <conditional name="omssa"> 819 <conditional name="comet_search">
258 <param name="omssa_selector" type="select" label="Run OMSSA search"> 820 <param name="comet_search_selector" type="select" label="Comet: Search Related">
259 <option value="yes" selected="True">Search with OMSSA</option> 821 <option value="yes">Set Search Parameters</option>
260 <option value="no">No OMSSA search</option> 822 <option value="no" selected="True">Keep Default Search Parameters</option>
261 </param> 823 </param>
262 <when value="no" /> 824 <when value="no" />
263 <when value="yes"> 825 <when value="yes">
264 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" /> 826 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
265 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/> 827 <option value="1">semi-specific</option>
266 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/> 828 <option value="2" selected="True">full-enzyme</option>
267 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" /> 829 <option value="8">unspecific N-term</option>
830 <option value="9">unspecific C-term</option>
831 </param>
832 <param name="comet_isotope_correction" label="Comet: Isotope Correction" type="select" help="Controls whether the peptide_mass_tolerance takes into account possible isotope errors in the precursor mass measurement">
833 <option value="0" selected="True">off</option>
834 <option value="1">-1,0,+1,+2,+3</option>
835 <option value="2">-8,-4,0,+4,+8</option>
836 </param>
837 <param name="comet_min_prec_mass" type="float" value="0.0"
838 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
839 <param name="comet_max_prec_mass" type="float" value="10000.0"
840 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
841 <param name="comet_num_matches" type="integer" value="10"
842 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
843 <param name="comet_max_frag_charge" type="integer" value="3"
844 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
845 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
846 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
847 <param name="comet_batch_size" type="integer" value="0"
848 label="Comet: Batch Size" help="0 means load and search all spectra at once, otherwise spectra are loaded and searched in batches of the number specified" />
849 <param name="comet_num_ptms" type="integer" value="10"
850 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
268 </when> 851 </when>
269 </conditional> 852 </conditional>
270 853 <!-- Fragment Ions Related parameters -->
271 <conditional name="msgf"> 854 <conditional name="comet_fragment_ions">
272 <param name="msgf_selector" type="select" label="Run MSGF search"> 855 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
273 <option value="yes" selected="True">Search with MSGF</option> 856 <option value="yes">Set Fragment Ions Parameters</option>
274 <option value="no">No MSGF search</option> 857 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
275 </param> 858 </param>
276 <when value="no" /> 859 <when value="no" />
277 <when value="yes"> 860 <when value="yes">
278 <param name="msgf_min_pep_length" type="integer" value="6" 861 <param name="comet_frag_bin_offset" type="float" value="0.4"
279 label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/> 862 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
280 <param name="msgf_max_pep_length" type="integer" value="30" 863 <param name="comet_sparse_matrix" type="boolean" truevalue="1" falsevalue="0" checked="true"
281 label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/> 864 label="Comet: Fragment Sparse Matrix" help="Controls whether or not internal sparse matrix data representation is used to lower memory usage" />
282 <param name="msgf_termini" type="select" format="text" 865 <param name="comet_theoretical_fragment_ions" type="integer" value="0"
283 label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2"> 866 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
284 <option value="0">0 (ie non-specific cleavage)</option>
285 <option value="1">1 (ie semi-tryptic cleavage)</option>
286 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
287 </param>
288 <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
289 </when> 867 </when>
290 </conditional> 868 </conditional>
291
292 <conditional name="myrimatch">
293 <param name="myrimatch_selector" type="select" label="Run MyriMatch search">
294 <option value="yes" selected="True">Search with MyriMatch</option>
295 <option value="no">No MyriMatch search</option>
296 </param>
297 <when value="no" />
298 <when value="yes">
299 </when>
300 </conditional>
301
302 <conditional name="comet">
303 <param name="comet_selector" type="select" label="Run Comet search">
304 <option value="yes" selected="True">Search with Comet</option>
305 <option value="no">No Comet search</option>
306 </param>
307 <when value="no" />
308 <when value="yes">
309 </when>
310 </conditional>
311
312 <conditional name="ms_amanda">
313 <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
314 <option value="yes">Search with MS Amanda</option>
315 <option value="no" selected="True">No MS Amanda search</option>
316 </param>
317 <when value="no" />
318 <when value="yes">
319 </when>
320 </conditional>
321
322 <conditional name="tide">
323 <param name="tide_selector" type="select" label="Run Tide search">
324 <option value="yes">Search with Tide</option>
325 <option value="no" selected="True">No Comet search</option>
326 </param>
327 <when value="no" />
328 <when value="yes">
329 </when>
330 </conditional>
331
332 </when> 869 </when>
333 </conditional> 870 </conditional>
334 </inputs> 871 </inputs>
335 <outputs> 872 <outputs>
336 <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> 873 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
337 </outputs> 874 </outputs>
338 <tests> 875 <tests>
876
877 <!-- Test that specifying non-default search engines works -->
339 <test> 878 <test>
340 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 879 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
341 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 880 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
342 <param name="precursor_ion_tol" value="100"/> 881 <param name="precursor_ion_tol" value="100"/>
343 <param name="fixed_modifications" value="carbamidomethyl c"/> 882 <param name="fixed_modifications" value="carbamidomethyl c"/>
344 <param name="variable_modifications" value="oxidation of m"/> 883 <param name="variable_modifications" value="oxidation of m"/>
345 <param name="min_charge" value="1"/> 884 <param name="min_charge" value="1"/>
346 <param name="max_charge" value="3"/> 885 <param name="max_charge" value="3"/>
347 <param name="advanced_type_selector" value="advanced"/> 886 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
348 <param name="xtandem_selector" value="yes"/> 887 <param name="xtandem.xtandem_advanced" value="yes"/>
349 <param name="xtandem_selector.xtandem_refine_selector" value="yes"/> 888 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
350 <param name="omssa_selector" value="no"/> 889
351 <param name="msgf_selector" value="yes"/> 890 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="600" />
352 <param name="ms_amanda_selector" value="no"/>
353 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" />
354 </test> 891 </test>
892
893 <!-- Test that search works with MSAmanda -->
894 <test>
895 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
896 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
897 <param name="precursor_ion_tol" value="100"/>
898 <param name="fixed_modifications" value="carbamidomethyl c"/>
899 <param name="variable_modifications" value="oxidation of m"/>
900 <param name="min_charge" value="1"/>
901 <param name="max_charge" value="3"/>
902 <param name="engines" value="MS_Amanda"/>
903
904 <output name="output" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="600" />
905 </test>
906
907
355 </tests> 908 </tests>
356 <help> 909 <help>
357 **What it does** 910 **What it does**
358 911
359 Runs multiple search engines on any number of MGF peak lists using the SearchGUI. 912 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
360 913 Default: X! Tandem, OMSSA and MS-GF+ are executed.
361 By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run. 914 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
362 915
363 </help> 916 </help>
364 <expand macro="citations" /> 917 <expand macro="citations" />
365 </tool> 918 </tool>