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comparison searchgui.xml @ 48:b72821cab1d7 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
author galaxyp
date Fri, 15 Jan 2021 14:05:46 +0000
parents a13e9d712194
children 560a08e0de13
comparison
equal deleted inserted replaced
47:5da80a2c0ef9 48:b72821cab1d7
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@">
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 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros_basic.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> 9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
10 <requirement type="package" version="3.0">zip</requirement> 10 <requirement type="package" version="3.0">zip</requirement>
11 </requirements> 11 </requirements>
12 <expand macro="stdio" /> 12 <expand macro="stdio" />
13 <command use_shared_home="false"> 13 <command use_shared_home="false">
14 <![CDATA[ 14 <![CDATA[
15 #from datetime import datetime 15 #from datetime import datetime
16 #import json
17 #import os
16 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s") 18 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
17 #set $samp_str = "Sample_%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")
18 #set $temp_stderr = "searchgui_stderr" 20 #set $temp_stderr = "searchgui_stderr"
19 #set $bin_dir = "bin" 21 #set $bin_dir = "bin"
20 22
25 27
26 echo "" > $temp_stderr && 28 echo "" > $temp_stderr &&
27 29
28 ## echo the search engines to run (single quotes important because X!Tandem) 30 ## echo the search engines to run (single quotes important because X!Tandem)
29 echo '$search_engines_options.engines'; 31 echo '$search_engines_options.engines';
30 echo 'DB: ${input_database.element_identifier} sequences: ${input_database.metadata.sequences}'; 32 echo 'DB: ${input_fasta_file.element_identifier} sequences: ${input_fasta_file.metadata.sequences}';
31 33
32 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present 34 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
33 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties; 35 echo 'searchgui.version=@SEARCHGUI_VERSION@' >> searchgui.properties;
34 36
35 #for $mgf in $peak_lists: 37 #for $peak_list_file in $peak_lists_files:
36 #set $input_name = $mgf.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf" 38 #set $input_name = ""
37 ln -s -f '${mgf}' '${input_name}'; 39 #if $peak_list_file.is_of_type("mgf"):
38 #set $encoded_id = $__app__.security.encode_id($mgf.id) 40 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mgf", "") + ".mgf"
39 echo 'Spectrums:${mgf.element_identifier}(API:${encoded_id})'; 41 #else if $peak_list_file.is_of_type("mzml"):
42 #set $input_name = $peak_list_file.element_identifier.split('/')[-1].replace(".mzml", "") + ".mzml"
43 #end if
44 ln -s -f '${peak_list_file}' '${input_name}';
45 #set $encoded_id = $__app__.security.encode_id($peak_list_file.id)
46 echo 'Spectrums:${peak_list_file.element_identifier}(API:${encoded_id})';
40 #end for 47 #end for
41 ##ln -s "${input_database}" input_database.fasta; 48
42 cp "${input_database}" input_database.fasta; 49 ## copy the input .par file to the working folder
43 50 cp '${input_parameters_file}' './SEARCHGUI_IdentificationParameters.par';
44 ########################################### 51
45 #### Set paths #### 52 ## copy the input .fasta file to the working folder
46 ########################################### 53 cp '${input_fasta_file}' './input_fasta_file.fasta';
47 echo 'Setting paths' && 54
48 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.PathSettingsCLI
49 --exec_dir="\$cwd/${bin_dir}"
50 -temp_folder \$cwd
51 -log \$cwd/searchgui.log 2>> $temp_stderr &&
52
53 ###########################################
54 #### Creating decoy database ####
55 ###########################################
56 #if $protein_database_options.create_decoy:
57 echo 'Creating decoy database.' &&
58 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
59 --exec_dir="\$cwd/${bin_dir}"
60 -in input_database.fasta
61 -decoy 2>> $temp_stderr &&
62 rm input_database.fasta &&
63 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
64 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
65 #end if
66
67 #####################################################
68 ## generate IdentificationParameters for SearchGUI ##
69 #####################################################
70 echo 'setting identification parameters' &&
71 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.IdentificationParametersCLI
72 --exec_dir="\$cwd/${bin_dir}"
73 -out SEARCHGUI_IdentificationParameters.par
74
75 @GENERAL_PARAMETERS@
76
77 -db input_database.fasta
78 $protein_database_options.use_gene_mapping
79 #if $protein_database_options.use_gene_mapping:
80 $protein_database_options.update_gene_mapping
81 #else:
82 -updateGeneMapping 0
83 #end if
84
85 #if $advanced_options.xtandem.xtandem_advanced == "yes"
86
87 -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
88 -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
89 -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
90 -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
91 -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
92 -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
93 -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
94 -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
95 -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
96 -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
97 -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
98 -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
99 -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
100 ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
101
102 #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
103 -xtandem_refine 1
104 -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
105 -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
106 -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
107 -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
108 -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
109 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
110 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
111
112 #end if
113 #else
114 -xtandem_output_spectra 1
115 #end if
116
117 #if $advanced_options.omssa.omssa_advanced == "yes"
118 -omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
119 -omssa_remove_prec ${advanced_options.omssa.remove_precursor}
120 -omssa_scale_prec ${advanced_options.omssa.scale_precursor}
121 -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
122 -omssa_memory ${advanced_options.omssa.omssa_memory}
123 -omssa_neutron ${advanced_options.omssa.omssa_neutron}
124 -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
125 -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
126 -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
127 -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
128 -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
129 -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
130 -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
131 -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
132 -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
133 -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
134 -omssa_methionine ${advanced_options.omssa.omssa_methionine}
135 -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
136 -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
137 -omssa_fraction ${advanced_options.omssa.omssa_fraction}
138 -omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
139 -omssa_charge ${advanced_options.omssa.omssa_charge}
140 -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
141 -omssa_forward ${advanced_options.omssa.omssa_forward}
142 -omssa_rewind ${advanced_options.omssa.omssa_rewind}
143 -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
144 -omssa_corr ${advanced_options.omssa.omssa_corr}
145 -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
146 -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
147 -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
148 -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
149 -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
150 -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
151 -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
152 -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
153 -omssa_format ${advanced_options.omssa.omssa_format}
154 #end if
155
156 #if $advanced_options.msgf.msgf_advanced == "yes"
157 -msgf_decoy ${advanced_options.msgf.msgf_decoy}
158 -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
159 -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
160 -msgf_termini ${advanced_options.msgf.msgf_termini}
161 -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
162 -msgf_instrument ${advanced_options.msgf.msgf_instrument}
163 -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
164 -msgf_protocol ${advanced_options.msgf.msgf_protocol}
165 -msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
166 -msgf_additional ${advanced_options.msgf.msgf_additional}
167 #end if
168
169 #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
170 -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
171 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
172 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
173 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
174 #end if
175
176 #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
177 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
178 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
179 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
180 -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
181 -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
182 -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
183 -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
184 -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
185 -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
186 -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
187 -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
188 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
189 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
190 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
191 -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
192 #end if
193
194
195 #* Not working in tests
196 #if $advanced_options.andromeda.andromeda_advanced == "yes"
197 -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
198 -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
199 -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
200 -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
201 -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
202 -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
203 -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
204 -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
205 -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
206 -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
207 -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
208 -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
209 -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
210 -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
211 -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
212 -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
213 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
214 #end if
215 *#
216
217 #if $advanced_options.tide.tide_advanced == "yes"
218 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
219 -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
220 #end if
221 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
222 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
223 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
224 -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
225 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
226 -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
227 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
228 -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
229 -tide_verbosity ${advanced_options.tide.tide_verbosity}
230 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
231 -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
232 -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
233 -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
234 -tide_max_psms ${advanced_options.tide.tide_max_psms}
235 -tide_compute_p ${advanced_options.tide.tide_compute_p}
236 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
237 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
238 -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
239 #end if
240 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
241 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
242 -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
243 -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
244 -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
245 -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
246 -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
247 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
248 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
249 -tide_concat ${advanced_options.tide.tide_concat}
250
251 #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
252 #for $format in $formats:
253 #if str($advanced_options.tide.tide_export).strip() == $format:
254 -$format 1
255 #else:
256 -$format 0
257 #end if
258
259 #end for
260
261 -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
262
263 #end if
264
265
266 #if $advanced_options.comet.comet_advanced == "yes"
267
268 #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
269 -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
270 -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
271
272 -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
273
274
275 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
276 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
277 #end if
278
279 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
280 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
281 #end if
282
283 -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
284 -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
285 #end if
286
287 #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
288 -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
289 -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
290 -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
291 -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
292 -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
293 -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
294 -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
295 -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
296 -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
297 #end if
298
299 #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
300 -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
301 -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
302 #end if
303 #end if
304
305 #if $advanced_options.directtag.directtag_advanced == "yes"
306 -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
307 -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
308 -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
309 -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
310 -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
311 -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
312 -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
313 -directag_charge_states ${advanced_options.directtag.directag_charge_states}
314 #if str($advanced_options.directtag.directag_output_suffix).strip() != '':
315 -directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
316 #end if
317 -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
318 -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
319 -directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
320 -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
321 -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
322 -directag_tag_length ${advanced_options.directtag.directag_tag_length}
323 -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
324 -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
325 -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
326 -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
327 -directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
328 #end if
329
330 #if $advanced_options.novor.novor_advanced == "yes"
331 -novor_fragmentation ${advanced_options.novor.novor_fragmentation}
332 -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
333 #end if
334
335 2> $temp_stderr)
336 &&
337 55
338 ################ 56 ################
339 ## Search CLI ## 57 ## Search CLI ##
340 ################ 58 ################
341 echo 'running search gui' && 59 echo 'running search gui' &&
342 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI 60 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
343 --exec_dir="\$cwd/${bin_dir}" 61 --exec_dir="\$cwd/${bin_dir}"
344 -spectrum_files \$cwd 62 -spectrum_files \$cwd
63 -fasta_file "\$cwd/input_fasta_file.fasta"
345 -output_folder \$cwd/output 64 -output_folder \$cwd/output
346 -id_params SEARCHGUI_IdentificationParameters.par 65 -id_params ./SEARCHGUI_IdentificationParameters.par
347 66
348 -threads "\${GALAXY_SLOTS:-12}" 67 -threads "\${GALAXY_SLOTS:-12}"
349 68
350 #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced' 69 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced'
351 -correct_titles "${advanced_options.searchgui_advanced.correct_titles}" 70 -correct_titles "${searchgui_advanced.correct_titles}"
352 $advanced_options.searchgui_advanced.missing_titles 71 $searchgui_advanced.missing_titles
353 -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}" 72 -mgf_splitting "${searchgui_advanced.mgf_splitting}"
354 -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}" 73 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
355 #end if 74 -output_gzip "${searchgui_advanced.output_gzip}"
356 75 #end if
357 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
358 ## the tree is generated afterwards in PeptideShaker
359 ## -protein_index 0
360
361 ##-makeblastdb_folder \$BLAST_ROOT_DIR
362 76
363 #set $engines_list = str($search_engines_options.engines).split(',') 77 #set $engines_list = str($search_engines_options.engines).split(',')
364 #if 'X!Tandem' in $engines_list: 78 #if 'X!Tandem' in $engines_list:
365 -xtandem 1 79 -xtandem 1
366 #else 80 #else
405 119
406 #if 'Andromeda' in $engines_list: 120 #if 'Andromeda' in $engines_list:
407 -andromeda 1 121 -andromeda 1
408 #else 122 #else
409 -andromeda 0 123 -andromeda 0
124 #end if
125
126 #if 'MetaMorpheus' in $engines_list:
127 -meta_morpheus 1
128 #else
129 -meta_morpheus 0
410 #end if 130 #end if
411 131
412 #if 'Novor' in $engines_list: 132 #if 'Novor' in $engines_list:
413 -novor 1 133 -novor 1
414 #else 134 #else
439 159
440 cat $temp_stderr 2>&1; 160 cat $temp_stderr 2>&1;
441 ]]> 161 ]]>
442 </command> 162 </command>
443 <inputs> 163 <inputs>
444 164 <param format="json" name="input_parameters_file" type="data" label="Identification Parameters file"/>
445 <param format="fasta" name="input_database" type="data" label="Protein Database" 165
446 help="Select FASTA database from history"/> 166 <param format="fasta" name="input_fasta_file" type="data" label="Fasta file"/>
447 <section name="protein_database_options" expanded="false" title="Protein Database Options"> 167
448 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" 168 <param name="peak_lists_files" format="mgf,mzml" type="data" multiple="true" label="Input Peak Lists"
449 label="Create a concatenated target/decoy database before running PeptideShaker" 169 help="Select appropriate MGF/MZML dataset(s) from history" />
450 help="Selecting this option will help PeptideShaker calculate FDR values" />
451 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
452 label="gene mappings will be used and saved along with the project (UniProt databases only)"
453 help="This should only be enabled for UniProt databaases" />
454 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
455 label="Update gene mappings automatically from Ensembl (UniProt databases only)"
456 help="This should only be enabled for UniProt databaases" />
457 </section>
458 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
459 help="Select appropriate MGF dataset(s) from history" />
460 170
461 <!-- Search Engine Selection --> 171 <!-- Search Engine Selection -->
462 <section name="search_engines_options" expanded="true" title="Search Engine Options"> 172 <section name="search_engines_options" expanded="true" title="Search Engine Options">
463 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> 173 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
464 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> 174 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm. OMSSA may not work into isolated environments like containers.</help>
465 <option value="X!Tandem" selected="True">X!Tandem</option> 175 <option value="X!Tandem" selected="True">X!Tandem</option>
466
467 <option value="MSGF" selected="True">MS-GF+</option> 176 <option value="MSGF" selected="True">MS-GF+</option>
468 <option value="OMSSA" selected="True">OMSSA</option> 177 <option value="OMSSA">OMSSA</option>
469 <option value="Comet">Comet</option> 178 <option value="Comet">Comet</option>
470 <option value="Tide">Tide</option> 179 <option value="Tide">Tide</option>
471 <option value="MyriMatch">MyriMatch</option> 180 <option value="MyriMatch">MyriMatch</option>
472 <option value="MS_Amanda">MS_Amanda</option> 181 <option value="MS_Amanda">MS_Amanda</option>
182 <!-- TODO: MetaMorpheus Waiting for support for dotnet in bioconda package -->
183 <!-- <option value="MetaMorpheus">MetaMorpheus</option> -->
473 <!-- Windows only 184 <!-- Windows only
474 <option value="Andromeda">Andromeda</option> 185 <option value="Andromeda">Andromeda</option>
475 --> 186 -->
476 <!-- New with version 3.0 187 <!-- New with version 3.0
477 --> 188 -->
481 <option value="Novor">Novor (Select for non-commercial use only)</option> 192 <option value="Novor">Novor (Select for non-commercial use only)</option>
482 <validator type="no_options" message="Please select at least one output file" /> 193 <validator type="no_options" message="Please select at least one output file" />
483 </param> 194 </param>
484 </section> 195 </section>
485 196
486 197 <conditional name="searchgui_advanced">
487 <!-- General Parameters --> 198 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
488 <expand macro="general_options"/> 199 <option value="basic" selected="True">Default</option>
489 200 <option value="advanced">Advanced</option>
490 201 </param>
491 <section name="advanced_options" expanded="false" title="Andvanced Options"> 202 <when value="basic" />
492 <!-- Optional Advanced SearchGUI Parameters --> 203 <when value="advanced">
493 <conditional name="searchgui_advanced">
494 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
495 <option value="basic" selected="True">Default</option>
496 <option value="advanced">Advanced</option>
497 </param>
498 <when value="basic" />
499 <when value="advanced">
500 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" 204 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
501 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> 205 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
502 <option value="0">no correction</option> 206 <option value="0">no correction</option>
503 <option value="1" selected="True">rename spectra</option> 207 <option value="1" selected="True">rename spectra</option>
504 <option value="2">delete spectra</option> 208 <option value="2">delete spectra</option>
505 </param> 209 </param>
506
507 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" 210 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
508 label="Add missing spectrum titles" help="(-missing_titles)"/> 211 label="Add missing spectrum titles" help="(-missing_titles)"/>
509
510 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" 212 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
511 help="Choose a smaller value if you are running on a machine with limited memory"/> 213 help="Choose a smaller value if you are running on a machine with limited memory"/>
512
513 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" 214 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
514 help="Choose a smaller value if you are running on a machine with limited memory"/> 215 help="Choose a smaller value if you are running on a machine with limited memory"/>
515 </when> 216 <param name="output_gzip" type="boolean" checked="true" truevalue="1" falsevalue="0"
516 </conditional> 217 label="Gzip result files"/>
517 218 </when>
518 <!-- X!TANDEM ADVANCED PARAMETERS --> 219 </conditional>
519 <conditional name="xtandem"> 220
520 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
521 <option value="yes">Advanced</option>
522 <option value="no" selected="True">Default</option>
523 </param>
524 <when value="no" />
525 <when value="yes">
526 <param name="xtandem_npeaks" type="integer" value="50"
527 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
528 <param name="xtandem_min_peaks" type="integer" value="15"
529 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
530 <param name="xtandem_min_frag_mz" type="integer" value="200"
531 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
532 <param name="xtandem_min_prec_mass" type="integer" value="200"
533 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
534 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
535 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
536 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
537 label="X!Tandem: Dynamic Range" value="100" type="integer" />
538 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
539 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
540 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
541 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
542 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
543 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
544 <param name="xtandem_evalue" help="Highest value for recorded peptides"
545 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
546 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
547 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
548 <param name="xtandem_output_sequences" help="Controls output of sequence information"
549 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
550 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
551 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
552 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
553
554 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
555 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
556 <option value="no" selected="True">Don't refine</option>
557 <option value="yes" >Use refinement</option>
558 </param>
559 <when value="no"/>
560 <when value="yes">
561 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
562 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
563 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
564 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
565 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
566 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
567 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
568 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
569 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
570 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
571 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
572 label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
573 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
574 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
575 </when>
576 </conditional>
577 </when>
578 </conditional>
579
580 <!-- OMSSA ADVANCED PARAMETERS -->
581 <conditional name="omssa">
582 <param name="omssa_advanced" type="select" label="OMSSA Options">
583 <option value="yes">Advanced</option>
584 <option value="no" selected="True">Default</option>
585 </param>
586 <when value="no" />
587 <when value="yes">
588 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
589 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
590 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
591 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
592
593 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
594 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
595 <param name="omssa_neutron" type="float" value="1446.94"
596 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
597 <param name="omssa_low_intensity" type="float" value="0.0"
598 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
599 <param name="omssa_high_intensity" type="float" value="0.2"
600 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
601 <param name="omssa_intensity_incr" type="float" value="0.0005"
602 label="OMSSA: Intensity Increment" help="Intensity increment" />
603 <param name="omssa_single_window_wd" type="integer" value="27"
604 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
605 <param name="omssa_double_window_wd" type="integer" value="14"
606 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
607 <param name="omssa_single_window_pk" type="integer" value="2"
608 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
609 <param name="omssa_double_window_pk" type="integer" value="2"
610 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
611 <param name="omssa_min_ann_int_pks" type="integer" value="6"
612 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
613 <param name="omssa_min_annotated_peaks" type="integer" value="2"
614 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
615 <param name="omssa_min_peaks" type="integer" value="4"
616 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
617 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
618 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
619 <param name="omssa_max_ladders" type="integer" value="128"
620 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
621 <param name="omssa_max_frag_charge" type="integer" value="2"
622 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
623 <param name="omssa_fraction" type="float" value="0.95"
624 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
625 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
626 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
627 <param name="omssa_charge" type="select"
628 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
629 <option value="0" >Minus</option>
630 <option value="1" selected="True">Plus</option>
631 </param>
632 <param name="omssa_prec_per_spectrum" type="integer" value="1"
633 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
634 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
635 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
636 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
637 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
638 <param name="omssa_max_frag_series" type="integer" value="100"
639 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
640 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
641 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
642 <param name="omssa_consecutive_p" type="float" value="0.5"
643 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
644 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
645 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
646 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
647 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
648 <param name="omssa_it_replace_evalue" type="float" value="0.01"
649 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
650 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
651 label="OMSSA: Remove Precursor" help="Remove precursors" />
652 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
653 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
654 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
655 label="OMSSA: Remove Precursor" help="Remove precursors" />
656 <param name="omssa_max_evalue" type="float" value="100"
657 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
658 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
659 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
660 <param name="omssa_it_replace_evalue" type="float" value="100"
661 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
662 <param name="omssa_hitlist_length" type="integer" value="0"
663 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
664 <param name="omssa_hitlist_charge" type="integer" value="30"
665 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
666 <param name="omssa_min_pep_length" type="integer" value="4"
667 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
668 <param name="omssa_max_pep_length" type="integer" value="40"
669 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
670 <param name="omssa_format" label="OMSSA output format" type="select" >
671 <option value="0" selected="True">OMX</option>
672 <option value="1" >CSV</option>
673 </param>
674 </when>
675 </conditional>
676
677 <!-- MS-GF+ ADVANCED PARAMETERS -->
678 <conditional name="msgf">
679 <param name="msgf_advanced" type="select" label="MSGF Options">
680 <option value="yes">Advanced</option>
681 <option value="no" selected="True">Default</option>
682 </param>
683 <when value="no" />
684 <when value="yes">
685 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
686 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
687 <param name="msgf_min_pep_length" type="integer" value="6"
688 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
689 <param name="msgf_max_pep_length" type="integer" value="30"
690 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
691 <param name="msgf_termini" type="select" format="txt"
692 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
693 <option value="0">0 (ie non-specific cleavage)</option>
694 <option value="1">1 (ie semi-tryptic cleavage)</option>
695 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
696 </param>
697 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
698
699 <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)">
700 <option value="0" selected="True">Low-res LCQ/LTQ</option>
701 <option value="1" >High-res LTQ</option>
702 <option value="2" >TOF</option>
703 <option value="3" >Q-Exactive</option>
704 </param>
705 <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
706 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
707 <option value="1" >CID</option>
708 <option value="2" >ETD</option>
709 <option value="3" >HCD</option>
710 </param>
711 <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">
712 <option value="0" selected="True">Automatic</option>
713 <option value="1" >Phosphorylation</option>
714 <option value="2" >iTRAQ</option>
715 <option value="3" >iTRAQPhospho</option>
716 <option value="4" >TMT</option>
717 <option value="5" >Standard</option>
718 </param>
719 <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" />
720 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
721 <option value="0" selected="True">output basic scores only</option>
722 <option value="1" >output additional features</option>
723 </param>
724 </when>
725 </conditional>
726
727 <!-- MS-AMANDA ADVANCED PARAMETERS -->
728 <conditional name="ms_amanda">
729 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
730 <option value="yes">Advanced</option>
731 <option value="no" selected="True">Default</option>
732 </param>
733 <when value="no" />
734 <when value="yes">
735 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
736 label="MS Amanda: Generate Decoys" help="generate decoys" />
737 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
738 help="MS Amanda instrument id option. Available ion types are listed here.">
739
740 <option value="b, y" selected="True">b, y</option>
741 <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
742 <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
743 <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
744 <option value="a, b, y" >a, b, y</option>
745 <option value="a, b, y, Imm" >a, b, y, Imm</option>
746 <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
747 <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
748 <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
749 <option value="b, y, INT" >b, y, INT</option>
750 <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
751 <option value="a, b, y, INT" >a, b, y, INT</option>
752 <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
753 <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
754 <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
755 <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
756
757 </param>
758 <param name="ms_amanda_max_rank" type="integer" value="10"
759 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
760 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
761 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
762 </when>
763 </conditional>
764
765
766 <!-- TIDE ADVANCED PARAMETERS -->
767 <conditional name="tide">
768 <param name="tide_advanced" type="select" label="TIDE Options">
769 <option value="yes">Advanced</option>
770 <option value="no" selected="True">Default</option>
771 </param>
772 <when value="no" />
773 <when value="yes">
774 <param name="tide_num_ptms" type="integer" value="" optional="true"
775 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
776 <param name="tide_num_ptms_per_type" type="integer" value="2"
777 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
778 <param name="tide_min_pep_length" type="integer" value="6"
779 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
780 <param name="tide_max_pep_length" type="integer" value="30"
781 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
782 <param name="tide_min_prec_mass" type="float" value="200.0"
783 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
784 <param name="tide_max_prec_mass" type="float" value="7200.0"
785 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
786 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
787 <option value="none" selected="True">none</option>
788 <option value="shuffle" >shuffle</option>
789 <option value="peptide-revers" >peptide-reverse</option>
790 <option value="protein-reverse" >protein-reverse</option>
791 </param>
792 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
793 <option value="N" >N</option>
794 <option value="C" >C</option>
795 <option value="NC" selected="True">NC</option>
796 <option value="non" >none</option>
797 </param>
798 <param name="tide_decoy_seed" type="integer" value="1"
799 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
800 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
801 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
802 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
803 <option value="0" >0</option>
804 <option value="10" >10</option>
805 <option value="20" >20</option>
806 <option value="30" selected="True">30</option>
807 <option value="40" >40</option>
808 <option value="50" >50</option>
809 <option value="60" >60</option>
810 </param>
811
812 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
813 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
814 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
815 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
816 <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">
817 <option value="full-digest" selected="True">full-digest</option>
818 <option value="partial-digest" >partial-digest</option>
819 </param>
820 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
821 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
822 <param name="tide_max_psms" type="integer" value="10"
823 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
824 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
825 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
826 <param name="tide_min_spectrum_mz" type="float" value="0.0"
827 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
828 <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
829 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
830 <param name="tide_min_spectrum_peaks" type="integer" value="20"
831 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
832 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
833 <option value="1" >1</option>
834 <option value="2" >2</option>
835 <option value="3" >3</option>
836 <option value="all" selected="True">all</option>
837 </param>
838 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
839 label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
840 <param name="tide_remove_prec_tol" type="float" value="1.5"
841 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
842 <param name="tide_progress_indicator" type="integer" value="1000"
843 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
844 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
845 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
846 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
847 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
848 <param name="tide_mz_bin_width" type="float" value="0.02"
849 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
850 <param name="tide_mz_bin_offset" type="float" value="0.0"
851 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
852 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
853 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
854
855 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
856 <option value="tide_export_text" selected="True">Text</option>
857 <option value="tide_export_sqt" >SQT</option>
858 <option value="tide_export_pepxml" >pepxml</option>
859 <option value="tide_export_mzid" >MzIdentML</option>
860 <option value="tide_export_pin" >Percolator input file</option>
861 </param>
862
863 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
864 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
865 </when>
866 </conditional>
867
868
869 <!-- MyriMatch ADVANCED PARAMETERS -->
870 <conditional name="myrimatch">
871 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
872 <option value="yes">Advanced</option>
873 <option value="no" selected="True">Default</option>
874 </param>
875 <when value="no" />
876 <when value="yes">
877 <param name="myrimatch_min_pep_length" type="integer" value="8"
878 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
879 <param name="myrimatch_max_pep_length" type="integer" value="30"
880 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
881 <param name="myrimatch_min_prec_mass" type="float" value="600.0"
882 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
883 <param name="myrimatch_max_prec_mass" type="float" value="5000.0"
884 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
885 <param name="myrimatch_num_matches" type="integer" value="10"
886 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
887 <param name="myrimatch_num_ptms" type="integer" value="2"
888 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
889 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
890 <option value="CID" selected="True">CID</option>
891 <option value="HCD" >HCD</option>
892 <option value="ETD" >ETD</option>
893 </param>
894 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
895 <option value="0">None required</option>
896 <option value="1">At least one</option>
897 <option value="2" selected="True" >Both</option>
898 </param>
899 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
900 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
901 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
902 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
903 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
904 label="MyriMatch: TIC cutoff percentage" help="Cumulative ion current of picked peaks divided by TIC >= this value for peaks to be retained (0.0 - 1.0)" />
905 <param name="myrimatch_intensity_classes" type="integer" value="3"
906 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
907 <param name="myrimatch_class_multiplier" type="integer" value="2"
908 label="MyriMatch: Class Size Multiplier" help="Has to do with previous option, this parameter controls the size of each class relative to the class above" />
909 <param name="myrimatch_num_batches" type="integer" value="50"
910 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
911 <param name="myrimatch_max_peak" type="integer" value="100"
912 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
913 </when>
914 </conditional>
915
916
917 <!-- Andromeda ADVANCED PARAMETERS -->
918 <!-- Windows only
919 <conditional name="andromeda">
920 <param name="andromeda_advanced" type="select" label="Andromeda Options">
921 <option value="yes">Advanced</option>
922 <option value="no" selected="True">Default</option>
923 </param>
924 <when value="no" />
925 <when value="yes">
926 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
927 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
928 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
929 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
930 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
931 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
932 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
933 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
934 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
935 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
936 <param name="andromeda_equal_il" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda whether I and L should be considered indistinguishable, default is: false" />
937 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
938 <option value="CID" selected="true">CID</option>
939 <option value="HCD">HCD</option>
940 <option value="EDT">EDT</option>
941 </param>
942 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
943 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
944 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
945 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
946 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
947 </when>
948 </conditional>
949 -->
950
951 <!-- Comet ADVANCED PARAMETERS -->
952 <conditional name="comet">
953 <param name="comet_advanced" type="select" label="Comet Options">
954 <option value="yes">Advanced</option>
955 <option value="no" selected="True">Default</option>
956 </param>
957 <when value="no" />
958 <when value="yes">
959 <!-- Spectrum Related parameters -->
960 <conditional name="comet_spectrum">
961 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
962 <option value="yes">Set Spectrum Parameters</option>
963 <option value="no" selected="True">Keep Default Spectrum Parameters</option>
964 </param>
965 <when value="no" />
966 <when value="yes">
967 <param name="comet_min_peaks" type="integer" value="10"
968 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
969 <param name="comet_min_peak_int" type="float" value="0.0"
970 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
971 <conditional name="comet_prec">
972 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
973 <option value="0" selected="True" >off</option>
974 <option value="1">on</option>
975 <option value="2">as expected for ETD/ECD spectra</option>
976 </param>
977 <when value="0" />
978 <when value="1">
979 <param name="comet_remove_prec_tol" type="float" value="1.5"
980 label="Comet: Remove Precursor Tolerance" />
981 </when>
982 <when value="2">
983 <param name="comet_remove_prec_tol" type="float" value="1.5"
984 label="Comet: Remove Precursor Tolerance" />
985 </when>
986 </conditional>
987 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
988 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" />
989 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
990 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" />
991 </when>
992 </conditional>
993 <!-- Search Related parameters -->
994 <conditional name="comet_search">
995 <param name="comet_search_selector" type="select" label="Comet: Search Related">
996 <option value="yes">Set Search Parameters</option>
997 <option value="no" selected="True">Keep Default Search Parameters</option>
998 </param>
999 <when value="no" />
1000 <when value="yes">
1001 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
1002 <option value="1">semi-specific</option>
1003 <option value="2" selected="True">full-enzyme</option>
1004 <option value="8">unspecific N-term</option>
1005 <option value="9">unspecific C-term</option>
1006 </param>
1007 <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">
1008 <option value="0" selected="True">off</option>
1009 <option value="1">-1,0,+1,+2,+3</option>
1010 <option value="2">-8,-4,0,+4,+8</option>
1011 </param>
1012 <param name="comet_min_prec_mass" type="float" value="0.0"
1013 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
1014 <param name="comet_max_prec_mass" type="float" value="10000.0"
1015 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
1016 <param name="comet_num_matches" type="integer" value="10"
1017 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
1018 <param name="comet_max_frag_charge" type="integer" value="3"
1019 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
1020 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
1021 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
1022 <param name="comet_batch_size" type="integer" value="0"
1023 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" />
1024 <param name="comet_num_ptms" type="integer" value="10"
1025 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
1026 </when>
1027 </conditional>
1028 <!-- Fragment Ions Related parameters -->
1029 <conditional name="comet_fragment_ions">
1030 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
1031 <option value="yes">Set Fragment Ions Parameters</option>
1032 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
1033 </param>
1034 <when value="no" />
1035 <when value="yes">
1036 <param name="comet_frag_bin_offset" type="float" value="0.4"
1037 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
1038 <param name="comet_theoretical_fragment_ions" type="integer" value="0"
1039 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
1040 </when>
1041 </conditional>
1042 </when>
1043 </conditional>
1044 <conditional name="directtag">
1045 <param name="directtag_advanced" type="select" label="DirectTag Options">
1046 <option value="yes">Advanced</option>
1047 <option value="no" selected="True">Default</option>
1048 </param>
1049 <when value="no" />
1050 <when value="yes">
1051 <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
1052 <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
1053 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
1054 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
1055 <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
1056 <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
1057 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
1058 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
1059 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
1060 <param name="directag_ms_charge_state" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag use charge state from M spectrum, default is false."/>
1061 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
1062 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
1063 <option value="0" selected="true">no deisotoping</option>
1064 <option value="1">precursor only</option>
1065 <option value="2">precursor and candidate</option>
1066 </param>
1067 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
1068 <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
1069 <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
1070 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
1071 <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
1072 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
1073 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
1074 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
1075 </when>
1076 </conditional>
1077
1078 <conditional name="novor">
1079 <param name="novor_advanced" type="select" label="Novor Options">
1080 <option value="yes">Advanced</option>
1081 <option value="no" selected="True">Default</option>
1082 </param>
1083 <when value="no" />
1084 <when value="yes">
1085 <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
1086 <option value="HCD" selected="True">HCD</option>
1087 <option value="CID">CID</option>
1088 </param>
1089 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
1090 <option value="FT" selected="True">FT</option>
1091 <option value="Trap" >Trap</option>
1092 <option value="TOF" >TOF</option>
1093 </param>
1094 </when>
1095 </conditional>
1096 </section>
1097 </inputs> 221 </inputs>
1098 <outputs> 222 <outputs>
1099 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> 223 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
1100 </outputs> 224 </outputs>
1101 <tests> 225 <tests>
1102 226
1103 <!-- Test that specifying non-default search engines works --> 227 <!-- Test that specifying non-default search engines with default parameters works -->
1104 <test> 228 <test>
1105 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 229 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
1106 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 230 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
231 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
232 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
233 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
234 </test>
235
236 <!-- Test that search works with MSAmanda with default parameters works-->
237 <test>
238 <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
239 <param name="input_parameters_file" value="Identification_Parameters_default.par"/>
240 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
241 <param name="engines" value="MS_Amanda"/>
242 <output name="searchgui_results" ftype="searchgui_archive">
243 <assert_contents>
244 <has_size value="635138" delta="5000"/>
245 </assert_contents>
246 </output>
247 </test>
248
249 <!-- Test that specifying non-default search engines with non-default parameters works -->
250 <test>
251 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
252 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
253 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
254 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
255 <output name="searchgui_results" ftype="searchgui_archive">
256 <assert_contents>
257 <has_size value="159330" delta="20000"/>
258 </assert_contents>
259 </output>
260 </test>
261
262 <!--
263 NOTE: Identification_Parameters_specific.par is equivalent to the default .par plus these parameters:
1107 <param name="precursor_ion_tol" value="100"/> 264 <param name="precursor_ion_tol" value="100"/>
1108 <param name="min_charge" value="1"/> 265 <param name="min_charge" value="1"/>
1109 <param name="max_charge" value="3"/> 266 <param name="max_charge" value="3"/>
1110 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1111 <param name="xtandem|xtandem_advanced" value="yes"/> 267 <param name="xtandem|xtandem_advanced" value="yes"/>
1112 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/> 268 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/>
1113 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 269 -->
1114 </test> 270
1115 <!-- Test that search works with MSAmanda --> 271 <!-- Test that specifying MsAmanda as search engine with non-default parameters works -->
1116 <test> 272 <test>
1117 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 273 <param name="peak_lists_files" value="searchgui_smallspectra.mgf"/>
1118 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 274 <param name="input_parameters_file" value="Identification_Parameters_specific.par"/>
1119 <param name="precursor_ion_tol" value="100"/> 275 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
1120 <param name="min_charge" value="1"/>
1121 <param name="max_charge" value="3"/>
1122 <param name="engines" value="MS_Amanda"/> 276 <param name="engines" value="MS_Amanda"/>
1123 <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 277 <output name="searchgui_results" ftype="searchgui_archive">
1124 </test> 278 <assert_contents>
1125 279 <has_size value="635158" delta="5000"/>
1126 <!-- Test that specifying non-default search engines works using modifications --> 280 </assert_contents>
1127 <test> 281 </output>
1128 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 282 </test>
1129 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 283
1130 <param name="precursor_ion_tol" value="100"/> 284 <!-- Test that specifying non-default search engines with default parameters works using modifications -->
1131 <param name="fixed_modifications" value="Carbamidomethylation of C"/> 285 <test>
1132 <param name="variable_modifications" value="Oxidation of M"/> 286 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
1133 <param name="min_charge" value="1"/> 287 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
1134 <param name="max_charge" value="3"/> 288 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
1135 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 289 <param name="engines" value="X!Tandem,MSGF,MyriMatch,Comet"/>
1136 <param name="xtandem|xtandem_advanced" value="yes"/> 290 <output name="searchgui_results" file="searchgui_tiny_result_default_4engines_modifications.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
1137 <param name="xtandem|xtandem_advanced|xtandem_refine_selector" value="yes"/> 291 </test>
1138 <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 292
1139 </test> 293 <!--
1140 <!-- Test that search works with MSAmanda - with modifications --> 294 NOTE: Identification_Parameters_default_modifications.par adds:
1141 <test> 295 - "Carbamidomethylation of C" as fixed modification
1142 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 296 - "Oxidation of M" as variable modification
1143 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/> 297 -->
1144 <param name="precursor_ion_tol" value="100"/> 298
1145 <param name="fixed_modifications" value="Carbamidomethylation of C"/> 299 <!-- Test that search works with MSAmanda with default default parameters - with modifications -->
1146 <param name="variable_modifications" value="Oxidation of M"/> 300 <test>
1147 <param name="min_charge" value="1"/> 301 <param name="peak_lists_files" value="searchgui_tinyspectra1.mgf"/>
1148 <param name="max_charge" value="3"/> 302 <param name="input_parameters_file" value="Identification_Parameters_default_modifications.par"/>
303 <param name="input_fasta_file" value="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" />
1149 <param name="engines" value="MS_Amanda"/> 304 <param name="engines" value="MS_Amanda"/>
1150 <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 305 <output name="searchgui_results" ftype="searchgui_archive">
1151 </test> 306 <assert_contents>
307 <has_size value="118136" delta="30000"/>
308 </assert_contents>
309 </output>
310 </test>
311
1152 </tests> 312 </tests>
1153 <help> 313 <help>
1154 **What it does** 314 **What it does**
1155 315
1156 Runs multiple search engines on any number of MGF peak lists using the SearchGUI. 316 Runs multiple search engines on any number of MGF peak lists using SearchGUI.
1157 Default: X! Tandem, OMSSA and MS-GF+ are executed. 317
1158 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed. 318 Default: X! Tandem and MS-GF+ are executed.
319
320 Optional: MyriMatch, MS-Amanda, OMSSA (it may not work into isolated environments like containers), Comet, Tide, DirecTag and Novor can be executed.
1159 321
1160 </help> 322 </help>
1161 <expand macro="citations" /> 323 <expand macro="citations" />
1162 </tool> 324 </tool>