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comparison searchgui.xml @ 2:eea7e945f479 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit b9d1c94d4c92009d99c5d4264e1085e7210208be-dirty
author jjohnson
date Thu, 12 Jul 2018 08:42:58 -0400
parents fa76abf69433
children
comparison
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1:fa76abf69433 2:eea7e945f479
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0"> 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.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 <macros> 5 <macros>
6 <import>macros_basic.xml</import> 6 <import>macros.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> 13 <command>
14 <![CDATA[ 14 <![CDATA[
15 #from datetime import datetime 15 #from datetime import datetime
16 #import json
17 #import os
18 #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")
19 #set $samp_str = "Sample_%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")
20 #set $temp_stderr = "searchgui_stderr" 18 #set $temp_stderr = "searchgui_stderr"
21 #set $bin_dir = "bin" 19 #set $bin_dir = "bin"
22 20
24 mkdir output_reports; 22 mkdir output_reports;
25 cwd=`pwd`; 23 cwd=`pwd`;
26 export HOME=\$cwd; 24 export HOME=\$cwd;
27 25
28 ## echo the search engines to run 26 ## echo the search engines to run
29 echo '$search_engines_options.engines'; 27 echo "$search_engines_options.engines";
28 echo "DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}";
30 29
31 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present 30 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present
32 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; 31 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties;
33 32
34 #for $mgf in $peak_lists: 33 #for $mgf in $peak_lists:
35 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf" 34 #set $input_name = $mgf.display_name.split('/')[-1].replace(".mgf", "") + ".mgf"
36 ln -s -f '${mgf}' '${input_name}'; 35 ln -s -f '${mgf}' '${input_name}';
37 #set $encoded_id = $__app__.security.encode_id($mgf.id) 36 #set $encoded_id = $__app__.security.encode_id($mgf.id)
38 echo 'Spectrums:${mgf.display_name}(API:${encoded_id}) '; 37 echo "Spectrums:${mgf.display_name}(API:${encoded_id}) ";
39 #end for 38 #end for
40 39 ##ln -s "${input_database}" input_database.fasta;
41 ## copy the input .par file to the working folder 40 cp "${input_database}" input_database.fasta;
42 cp '${input_zip}' './input_par_fasta.zip'; 41
43 echo '-.zip source file:'; 42 ###########################################
44 echo '${input_zip}'; 43 #### Creating decoy database ####
45 44 ###########################################
46 45 #if $protein_database_options.create_decoy:
47 ## Necessary for executing tests. Specific par files need to be uncompressed to be used by the tool. 46 echo "Creating decoy database.";
48 jar xvf './input_par_fasta.zip' 'Identification_Parameters_default.par' 'searchgui_tinydb1_concatenated_target_decoy.fasta'; 47 searchgui eu.isas.searchgui.cmd.FastaCLI --exec_dir="\$cwd/${bin_dir}" -in input_database.fasta -decoy &&
49 jar xvf './input_par_fasta.zip' Identification_Parameters_specific.par searchgui_tinydb1_concatenated_target_decoy.fasta; 48 rm input_database.fasta &&
50 if [ -f ./Identification_Parameters_default.par ];then 49 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
51 mv ./Identification_Parameters_default.par ./SEARCHGUI_IdentificationParameters.par; 50 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
52 fi; 51 #end if
53 if [ -f ./Identification_Parameters_specific.par ];then 52 @ENZYMESCLI@
54 mv './Identification_Parameters_specific.par' './SEARCHGUI_IdentificationParameters.par'; 53 #####################################################
55 fi; 54 ## generate IdentificationParameters for SearchGUI ##
56 55 #####################################################
57 ## By default we will always try to uncompress SEARCHGUI_IdentificationParameters.par and input_database.fasta 56 (searchgui eu.isas.searchgui.cmd.IdentificationParametersCLI
58 jar xvf './input_par_fasta.zip' SEARCHGUI_IdentificationParameters.par input_database.fasta; 57 --exec_dir="\$cwd/${bin_dir}"
59 58 -out SEARCHGUI_IdentificationParameters.par
59
60 @GENERAL_PARAMETERS@
61
62 -db input_database.fasta
63 $protein_database_options.use_gene_mapping
64 #if $protein_database_options.use_gene_mapping:
65 $protein_database_options.update_gene_mapping
66 #else:
67 -updateGeneMapping 0
68 #end if
69
70 #if $advanced_options.xtandem.xtandem_advanced == "yes"
71
72 -xtandem_npeaks ${advanced_options.xtandem.xtandem_npeaks}
73 -xtandem_min_peaks ${advanced_options.xtandem.xtandem_min_peaks}
74 -xtandem_min_frag_mz ${advanced_options.xtandem.xtandem_min_frag_mz}
75 -xtandem_min_prec_mass ${advanced_options.xtandem.xtandem_min_prec_mass}
76 -xtandem_noise_suppr ${advanced_options.xtandem.xtandem_noise_suppr}
77 -xtandem_dynamic_range ${advanced_options.xtandem.xtandem_dynamic_range}
78 -xtandem_quick_acetyl ${advanced_options.xtandem.xtandem_quick_acetyl}
79 -xtandem_quick_pyro ${advanced_options.xtandem.xtandem_quick_pyro}
80 -xtandem_stp_bias ${advanced_options.xtandem.xtandem_stp_bias}
81 -xtandem_evalue ${advanced_options.xtandem.xtandem_evalue}
82 -xtandem_output_proteins ${advanced_options.xtandem.xtandem_output_proteins}
83 -xtandem_output_sequences ${advanced_options.xtandem.xtandem_output_sequences}
84 -xtandem_output_spectra ${advanced_options.xtandem.xtandem_output_spectra}
85 ## -xtandem_skyline_path ${advanced_options.xtandem.xtandem_skyline_path}
86
87 #if $advanced_options.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
88 -xtandem_refine 1
89 -xtandem_refine_unc ${advanced_options.xtandem.xtandem_refine.xtandem_refine_unc}
90 -xtandem_refine_semi ${advanced_options.xtandem.xtandem_refine.xtandem_refine_semi}
91 -xtandem_refine_p_mut ${advanced_options.xtandem.xtandem_refine.xtandem_refine_p_mut}
92 -xtandem_refine_snaps ${advanced_options.xtandem.xtandem_refine.xtandem_refine_snaps}
93 -xtandem_refine_spec_synt ${advanced_options.xtandem.xtandem_refine.xtandem_refine_spec_synt}
94 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_pot}
95 -xtandem_refine_pot ${advanced_options.xtandem.xtandem_refine.xtandem_refine_evalue}
96
97 #end if
98 #else
99 -xtandem_output_spectra 1
100 #end if
101
102 #if $advanced_options.omssa.omssa_advanced == "yes"
103 -omssa_hitlist_length ${advanced_options.omssa.hitlist_length}
104 -omssa_remove_prec ${advanced_options.omssa.remove_precursor}
105 -omssa_scale_prec ${advanced_options.omssa.scale_precursor}
106 -omssa_estimate_charge ${advanced_options.omssa.estimate_charge}
107 -omssa_memory ${advanced_options.omssa.omssa_memory}
108 -omssa_neutron ${advanced_options.omssa.omssa_neutron}
109 -omssa_low_intensity "${advanced_options.omssa.omssa_low_intensity}"
110 -omssa_high_intensity ${advanced_options.omssa.omssa_high_intensity}
111 -omssa_intensity_incr ${advanced_options.omssa.omssa_intensity_incr}
112 -omssa_single_window_wd ${advanced_options.omssa.omssa_single_window_wd}
113 -omssa_double_window_wd ${advanced_options.omssa.omssa_double_window_wd}
114 -omssa_single_window_pk ${advanced_options.omssa.omssa_single_window_pk}
115 -omssa_double_window_pk ${advanced_options.omssa.omssa_double_window_pk}
116 -omssa_min_ann_int_pks ${advanced_options.omssa.omssa_min_ann_int_pks}
117 -omssa_min_annotated_peaks ${advanced_options.omssa.omssa_min_annotated_peaks}
118 -omssa_min_peaks ${advanced_options.omssa.omssa_min_peaks}
119 -omssa_methionine ${advanced_options.omssa.omssa_methionine}
120 -omssa_max_ladders ${advanced_options.omssa.omssa_max_ladders}
121 -omssa_max_frag_charge ${advanced_options.omssa.omssa_max_frag_charge}
122 -omssa_fraction ${advanced_options.omssa.omssa_fraction}
123 -omssa_plus_one ${advanced_options.omssa.omssa_plus_one}
124 -omssa_charge ${advanced_options.omssa.omssa_charge}
125 -omssa_prec_per_spectrum ${advanced_options.omssa.omssa_prec_per_spectrum}
126 -omssa_forward ${advanced_options.omssa.omssa_forward}
127 -omssa_rewind ${advanced_options.omssa.omssa_rewind}
128 -omssa_max_frag_series ${advanced_options.omssa.omssa_max_frag_series}
129 -omssa_corr ${advanced_options.omssa.omssa_corr}
130 -omssa_consecutive_p ${advanced_options.omssa.omssa_consecutive_p}
131 -omssa_it_sequence_evalue ${advanced_options.omssa.omssa_it_sequence_evalue}
132 -omssa_it_spectrum_evalue ${advanced_options.omssa.omssa_it_spectrum_evalue}
133 -omssa_it_replace_evalue ${advanced_options.omssa.omssa_it_replace_evalue}
134 -omssa_max_evalue ${advanced_options.omssa.omssa_max_evalue}
135 -omssa_hitlist_charge ${advanced_options.omssa.omssa_hitlist_charge}
136 -omssa_min_pep_length ${advanced_options.omssa.omssa_min_pep_length}
137 -omssa_max_pep_length ${advanced_options.omssa.omssa_max_pep_length}
138 -omssa_format ${advanced_options.omssa.omssa_format}
139 #end if
140
141 #if $advanced_options.msgf.msgf_advanced == "yes"
142 -msgf_decoy ${advanced_options.msgf.msgf_decoy}
143 -msgf_min_pep_length ${advanced_options.msgf.msgf_min_pep_length}
144 -msgf_max_pep_length ${advanced_options.msgf.msgf_max_pep_length}
145 -msgf_termini ${advanced_options.msgf.msgf_termini}
146 -msgf_num_ptms ${advanced_options.msgf.msgf_num_ptms}
147 -msgf_instrument ${advanced_options.msgf.msgf_instrument}
148 -msgf_fragmentation ${advanced_options.msgf.msgf_fragmentation}
149 -msgf_protocol ${advanced_options.msgf.msgf_protocol}
150 -msgf_num_matches ${advanced_options.msgf.msgf_num_matches}
151 -msgf_additional ${advanced_options.msgf.msgf_additional}
152 #end if
153
154 #if $advanced_options.ms_amanda.ms_amanda_advanced == "yes"
155 -ms_amanda_decoy ${advanced_options.ms_amanda.ms_amanda_decoy}
156 -ms_amanda_instrument "${advanced_options.ms_amanda.ms_amanda_instrument}"
157 -ms_amanda_max_rank ${advanced_options.ms_amanda.ms_amanda_max_rank}
158 -ms_amanda_mono ${advanced_options.ms_amanda.ms_amanda_mono}
159 #end if
160
161 #if $advanced_options.myrimatch.myrimatch_advanced == "yes"
162 -myrimatch_min_pep_length ${advanced_options.myrimatch.myrimatch_min_pep_length}
163 -myrimatch_max_pep_length ${advanced_options.myrimatch.myrimatch_max_pep_length}
164 -myrimatch_min_prec_mass ${advanced_options.myrimatch.myrimatch_min_prec_mass}
165 -myrimatch_max_prec_mass ${advanced_options.myrimatch.myrimatch_max_prec_mass}
166 -myrimatch_num_matches ${advanced_options.myrimatch.myrimatch_num_matches}
167 -myrimatch_num_ptms ${advanced_options.myrimatch.myrimatch_num_ptms}
168 -myrimatch_fragmentation ${advanced_options.myrimatch.myrimatch_fragmentation}
169 -myrimatch_termini ${advanced_options.myrimatch.myrimatch_termini}
170 -myrimatch_plus_three ${advanced_options.myrimatch.myrimatch_plus_three}
171 -myrimatch_xcorr ${advanced_options.myrimatch.myrimatch_xcorr}
172 -myrimatch_tic_cutoff ${advanced_options.myrimatch.myrimatch_tic_cutoff}
173 -myrimatch_intensity_classes ${advanced_options.myrimatch.myrimatch_intensity_classes}
174 -myrimatch_class_multiplier ${advanced_options.myrimatch.myrimatch_class_multiplier}
175 -myrimatch_num_batches ${advanced_options.myrimatch.myrimatch_num_batches}
176 -myrimatch_max_peak ${advanced_options.myrimatch.myrimatch_max_peak}
177 #end if
178
179
180 #* Not working in tests
181 #if $advanced_options.andromeda.andromeda_advanced == "yes"
182 -andromeda_max_pep_mass ${advanced_options.andromeda.andromeda_max_pep_mass}
183 -andromeda_max_comb ${advanced_options.andromeda.andromeda_max_comb}
184 -andromeda_top_peaks ${advanced_options.andromeda.andromeda_top_peaks}
185 -andromeda_top_peaks_window ${advanced_options.andromeda.andromeda_top_peaks_window}
186 -andromeda_incl_water ${advanced_options.andromeda.andromeda_incl_water}
187 -andromeda_incl_ammonia ${advanced_options.andromeda.andromeda_incl_ammonia}
188 -andromeda_neutral_losses ${advanced_options.andromeda.andromeda_neutral_losses}
189 -andromeda_fragment_all ${advanced_options.andromeda.andromeda_fragment_all}
190 -andromeda_emp_correction ${advanced_options.andromeda.andromeda_emp_correction}
191 -andromeda_higher_charge ${advanced_options.andromeda.andromeda_higher_charge}
192 -andromeda_equal_il ${advanced_options.andromeda.andromeda_equal_il}
193 -andromeda_frag_method ${advanced_options.andromeda.andromeda_frag_method}
194 -andromeda_max_mods ${advanced_options.andromeda.andromeda_max_mods}
195 -andromeda_min_pep_length ${advanced_options.andromeda.andromeda_min_pep_length}
196 -andromeda_max_pep_length ${advanced_options.andromeda.andromeda_max_pep_length}
197 -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms}
198 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode}
199 #end if
200 *#
201
202 #if $advanced_options.tide.tide_advanced == "yes"
203 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
204 -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz}
205 #end if
206 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type}
207 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length}
208 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length}
209 -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass}
210 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass}
211 -tide_decoy_format ${advanced_options.tide.tide_decoy_format}
212 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals}
213 -tide_print_peptides ${advanced_options.tide.tide_print_peptides}
214 -tide_verbosity ${advanced_options.tide.tide_verbosity}
215 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic}
216 -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term}
217 -tide_digestion_type ${advanced_options.tide.tide_digestion_type}
218 -tide_compute_sp ${advanced_options.tide.tide_compute_sp}
219 -tide_max_psms ${advanced_options.tide.tide_max_psms}
220 -tide_compute_p ${advanced_options.tide.tide_compute_p}
221 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz}
222 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '':
223 -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz}
224 #end if
225 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks}
226 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges}
227 -tide_remove_prec ${advanced_options.tide.tide_remove_prec}
228 -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol}
229 -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator}
230 -tide_use_flanking ${advanced_options.tide.tide_use_flanking}
231 -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses}
232 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width}
233 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset}
234 -tide_concat ${advanced_options.tide.tide_concat}
235
236 #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"]
237 #for $format in $formats:
238 #if str($advanced_options.tide.tide_export).strip() == $format:
239 -$format 1
240 #else:
241 -$format 0
242 #end if
243
244 #end for
245
246 -tide_remove_temp ${advanced_options.tide.tide_remove_temp}
247
248 #end if
249
250
251 #if $advanced_options.comet.comet_advanced == "yes"
252
253 #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes"
254 -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks}
255 -comet_min_peak_int ${advanced_options.comet.comet_spectrum.comet_min_peak_int}
256
257 -comet_remove_prec ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec}
258
259
260 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "1"
261 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
262 #end if
263
264 #if $advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec == "2"
265 -comet_remove_prec_tol ${advanced_options.comet.comet_spectrum.comet_prec.comet_remove_prec_tol}
266 #end if
267
268 -comet_clear_mz_range_lower ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_lower}
269 -comet_clear_mz_range_upper ${advanced_options.comet.comet_spectrum.comet_clear_mz_range_upper}
270 #end if
271
272 #if $advanced_options.comet.comet_search.comet_search_selector == "yes"
273 -comet_enzyme_type ${advanced_options.comet.comet_search.comet_enzyme_type}
274 -comet_isotope_correction ${advanced_options.comet.comet_search.comet_isotope_correction}
275 -comet_min_prec_mass ${advanced_options.comet.comet_search.comet_min_prec_mass}
276 -comet_max_prec_mass ${advanced_options.comet.comet_search.comet_max_prec_mass}
277 -comet_num_matches ${advanced_options.comet.comet_search.comet_num_matches}
278 -comet_max_frag_charge ${advanced_options.comet.comet_search.comet_max_frag_charge}
279 -comet_remove_meth ${advanced_options.comet.comet_search.comet_remove_meth}
280 -comet_batch_size ${advanced_options.comet.comet_search.comet_batch_size}
281 -comet_num_ptms ${advanced_options.comet.comet_search.comet_num_ptms}
282 #end if
283
284 #if $advanced_options.comet.comet_fragment_ions.comet_fragment_ions_selector == "yes"
285 -comet_frag_bin_offset ${advanced_options.comet.comet_fragment_ions.comet_frag_bin_offset}
286 -comet_theoretical_fragment_ions ${advanced_options.comet.comet_fragment_ions.comet_theoretical_fragment_ions}
287 #end if
288 #end if
289
290 #if $advanced_options.directtag.directtag_advanced == "yes"
291 -directag_tic_cutoff ${advanced_options.directtag.directag_tic_cutoff}
292 -directag_max_peak_count ${advanced_options.directtag.directag_max_peak_count}
293 -directag_intensity_classes ${advanced_options.directtag.directag_intensity_classes}
294 -directag_adjust_precursor ${advanced_options.directtag.directag_adjust_precursor}
295 -directag_min_adjustment ${advanced_options.directtag.directag_min_adjustment}
296 -directag_max_adjustment ${advanced_options.directtag.directag_max_adjustment}
297 -directag_adjustment_step ${advanced_options.directtag.directag_adjustment_step}
298 -directag_charge_states ${advanced_options.directtag.directag_charge_states}
299 #if str($advanced_options.directtag.directag_output_suffix).strip() != '':
300 -directag_output_suffix ${advanced_options.directtag.directag_output_suffix}
301 #end if
302 -directag_ms_charge_state ${advanced_options.directtag.directag_ms_charge_state}
303 -directag_duplicate_spectra ${advanced_options.directtag.directag_duplicate_spectra}
304 -directag_deisotoping ${advanced_options.directtag.directag_deisotoping}
305 -directag_isotope_tolerance ${advanced_options.directtag.directag_isotope_tolerance}
306 -directag_complement_tolerance ${advanced_options.directtag.directag_complement_tolerance}
307 -directag_tag_length ${advanced_options.directtag.directag_tag_length}
308 -directag_max_var_mods ${advanced_options.directtag.directag_max_var_mods}
309 -directag_max_tag_count ${advanced_options.directtag.directag_max_tag_count}
310 -directag_intensity_weight ${advanced_options.directtag.directag_intensity_weight}
311 -directag_fidelity_weight ${advanced_options.directtag.directag_fidelity_weight}
312 -directag_complement_weight ${advanced_options.directtag.directag_complement_weight}
313 #end if
314
315 #if $advanced_options.novor.novor_advanced == "yes"
316 -novor_fragmentation ${advanced_options.novor.novor_fragmentation}
317 -novor_mass_analyzer ${advanced_options.novor.novor_mass_analyzer}
318 #end if
319
320 2> $temp_stderr)
321 &&
60 322
61 ################ 323 ################
62 ## Search CLI ## 324 ## Search CLI ##
63 ################ 325 ################
64 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI 326 (searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.SearchCLI
65 --exec_dir="\$cwd/${bin_dir}" 327 --exec_dir="\$cwd/${bin_dir}"
66 -temp_folder `pwd` 328 -temp_folder `pwd`
67 -spectrum_files \$cwd 329 -spectrum_files \$cwd
68 -output_folder \$cwd/output 330 -output_folder \$cwd/output
69 -id_params ./SEARCHGUI_IdentificationParameters.par 331 @ENZYME_CONFIGUTRATION@
332 -id_params SEARCHGUI_IdentificationParameters.par
70 333
71 -threads "\${GALAXY_SLOTS:-12}" 334 -threads "\${GALAXY_SLOTS:-12}"
72 335
73 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' 336 #if $advanced_options.searchgui_advanced.searchgui_advanced_selector == 'advanced'
74 -correct_titles "${searchgui_advanced.correct_titles}" 337 -correct_titles "${advanced_options.searchgui_advanced.correct_titles}"
75 $searchgui_advanced.missing_titles 338 $advanced_options.searchgui_advanced.missing_titles
76 -mgf_splitting "${searchgui_advanced.mgf_splitting}" 339 -mgf_splitting "${advanced_options.searchgui_advanced.mgf_splitting}"
77 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" 340 -mgf_spectrum_count "${advanced_options.searchgui_advanced.mgf_spectrum_count}"
78 #end if 341 #end if
79 342
80 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created 343 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
81 ## the tree is generated afterwards in PeptideShaker 344 ## the tree is generated afterwards in PeptideShaker
82 ## -protein_index 0 345 ## -protein_index 0
164 cat $temp_stderr 2>&1; 427 cat $temp_stderr 2>&1;
165 (exit \$exit_code_for_galaxy) 428 (exit \$exit_code_for_galaxy)
166 ]]> 429 ]]>
167 </command> 430 </command>
168 <inputs> 431 <inputs>
169 <param format="zip" name="input_zip" type="data" label="Identification Parameters and fasta file" 432
170 help="Select a zip file with Identification Parameters (.par) and a fasta file from history"/> 433 <param format="fasta" name="input_database" type="data" label="Protein Database"
171 434 help="Select FASTA database from history"/>
435 <section name="protein_database_options" expanded="false" title="Protein Database Options">
436 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
437 label="Create a concatenated target/decoy database before running PeptideShaker"
438 help="Selecting this option will help PeptideShaker calculate FDR values" />
439 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
440 label="gene mappings will be used and saved along with the project (UniProt databases only)"
441 help="This should only be enabled for UniProt databaases" />
442 <param name="update_gene_mapping" type="boolean" truevalue="-updateGeneMapping 1" falsevalue="-updateGeneMapping 0" checked="false"
443 label="Update gene mappings automatically from Ensembl (UniProt databases only)"
444 help="This should only be enabled for UniProt databaases" />
445 </section>
172 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" 446 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
173 help="Select appropriate MGF dataset(s) from history" /> 447 help="Select appropriate MGF dataset(s) from history" />
174 448
175 <!-- Search Engine Selection --> 449 <!-- Search Engine Selection -->
176 <section name="search_engines_options" expanded="true" title="Search Engine Options"> 450 <section name="search_engines_options" expanded="true" title="Search Engine Options">
177 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> 451 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
178 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> 452 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
179 <option value="X!Tandem" selected="True">X!Tandem</option> 453 <option value="X!Tandem" selected="True">X!Tandem</option>
454
180 <option value="MSGF" selected="True">MS-GF+</option> 455 <option value="MSGF" selected="True">MS-GF+</option>
181 <option value="OMSSA" selected="True">OMSSA</option> 456 <option value="OMSSA" selected="True">OMSSA</option>
182 <option value="Comet">Comet</option> 457 <option value="Comet">Comet</option>
183 <option value="Tide">Tide</option> 458 <option value="Tide">Tide</option>
184 <option value="MyriMatch">MyriMatch</option> 459 <option value="MyriMatch">MyriMatch</option>
194 <option value="Novor">Novor (Select for non-commercial use only)</option> 469 <option value="Novor">Novor (Select for non-commercial use only)</option>
195 <validator type="no_options" message="Please select at least one output file" /> 470 <validator type="no_options" message="Please select at least one output file" />
196 </param> 471 </param>
197 </section> 472 </section>
198 473
199 <conditional name="searchgui_advanced"> 474
200 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options"> 475 <!-- General Parameters -->
201 <option value="basic" selected="True">Default</option> 476 <expand macro="general_options"/>
202 <option value="advanced">Advanced</option> 477
203 </param> 478
204 <when value="basic" /> 479 <section name="advanced_options" expanded="false" title="Andvanced Options">
205 <when value="advanced"> 480 <!-- Optional Advanced SearchGUI Parameters -->
206 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?" 481 <conditional name="searchgui_advanced">
207 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option"> 482 <param name="searchgui_advanced_selector" type="select" label="SearchGUI Options">
208 <option value="0">no correction</option> 483 <option value="basic" selected="True">Default</option>
209 <option value="1" selected="True">rename spectra</option> 484 <option value="advanced">Advanced</option>
210 <option value="2">delete spectra</option> 485 </param>
211 </param> 486 <when value="basic" />
212 487 <when value="advanced">
213 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0" 488 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
214 label="Add missing spectrum titles" help="(-missing_titles)"/> 489 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
215 490 <option value="0">no correction</option>
216 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf" 491 <option value="1" selected="True">rename spectra</option>
217 help="Choose a smaller value if you are running on a machine with limited memory"/> 492 <option value="2">delete spectra</option>
218 493 </param>
219 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting" 494
220 help="Choose a smaller value if you are running on a machine with limited memory"/> 495 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
221 </when> 496 label="Add missing spectrum titles" help="(-missing_titles)"/>
222 </conditional> 497
223 498 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
499 help="Choose a smaller value if you are running on a machine with limited memory"/>
500
501 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
502 help="Choose a smaller value if you are running on a machine with limited memory"/>
503 </when>
504 </conditional>
505
506 <!-- X!TANDEM ADVANCED PARAMETERS -->
507 <conditional name="xtandem">
508 <param name="xtandem_advanced" type="select" label="X!Tandem Options">
509 <option value="yes">Advanced</option>
510 <option value="no" selected="True">Default</option>
511 </param>
512 <when value="no" />
513 <when value="yes">
514 <param name="xtandem_npeaks" type="integer" value="50"
515 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
516 <param name="xtandem_min_peaks" type="integer" value="15"
517 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
518 <param name="xtandem_min_frag_mz" type="integer" value="200"
519 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
520 <param name="xtandem_min_prec_mass" type="integer" value="200"
521 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
522 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
523 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
524 <param name="xtandem_dynamic_range" help="Sets the dynamic range for scoring spectra"
525 label="X!Tandem: Dynamic Range" value="100" type="integer" />
526 <param name="xtandem_quick_acetyl" help="Protein N-terminal modification detection"
527 label="X!Tandem: Quick Acetyl" type="boolean" truevalue="1" falsevalue="0" checked="true" />
528 <param name="xtandem_quick_pyro" help="Peptide N-terminus cyclization detection"
529 label="X!Tandem: Quick Pyrolidone" type="boolean" truevalue="1" falsevalue="0" checked="true" />
530 <param name="xtandem_stp_bias" help="Interpretation of peptide phosphorylation models"
531 label="X!Tandem: Protein stP Bias" type="boolean" truevalue="1" falsevalue="0" checked="false" />
532 <param name="xtandem_evalue" help="Highest value for recorded peptides"
533 label="X!Tandem: Maximum Valid Expectation Value" type="float" value="0.01" />
534 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
535 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
536 <param name="xtandem_output_sequences" help="Controls output of sequence information"
537 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
538 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
539 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
540 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="txt" help="Path to a spectrum data file for use by skyline." -->
541
542 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
543 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
544 <option value="no" selected="True">Don't refine</option>
545 <option value="yes" >Use refinement</option>
546 </param>
547 <when value="no"/>
548 <when value="yes">
549 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0" checked="true"
550 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
551 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0" checked="false"
552 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
553 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0" checked="false"
554 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
555 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0" checked="true"
556 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
557 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0" checked="true"
558 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
559 <param name="xtandem_refine_pot" type="boolean" truevalue="1" falsevalue="0" checked="false"
560 label="X!Tandem: Use potential modifications, refinement" help="Controls the use of refinement modifications in all refinement modules."/>
561 <param name="xtandem_refine_evalue" help="Highest value for recorded peptides during refinement"
562 label="X!Tandem: Maximum Valid Expectation Value, refinement" type="float" value="0.01" />
563 </when>
564 </conditional>
565 </when>
566 </conditional>
567
568 <!-- OMSSA ADVANCED PARAMETERS -->
569 <conditional name="omssa">
570 <param name="omssa_advanced" type="select" label="OMSSA Options">
571 <option value="yes">Advanced</option>
572 <option value="no" selected="True">Default</option>
573 </param>
574 <when value="no" />
575 <when value="yes">
576 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
577 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
578 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
579 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
580
581 <param name="omssa_memory" type="boolean" truevalue="1" falsevalue="0" checked="true"
582 label="OMSSA: Map Sequences in Memory" help="Use memory mapped sequence libraries" />
583 <param name="omssa_neutron" type="float" value="1446.94"
584 label="OMSSA: Neutron Mass" help="Mass after which OMSSA should consider neutron exact mass" />
585 <param name="omssa_low_intensity" type="float" value="0.0"
586 label="OMSSA: Low Intensity Cutoff" help="Low intensity cutoff as a fraction of max peak" />
587 <param name="omssa_high_intensity" type="float" value="0.2"
588 label="OMSSA: High Intensity Cutoff" help="High intensity cutoff as a fraction of max peak" />
589 <param name="omssa_intensity_incr" type="float" value="0.0005"
590 label="OMSSA: Intensity Increment" help="Intensity increment" />
591 <param name="omssa_single_window_wd" type="integer" value="27"
592 label="OMSSA: Single Charge Window Width" help="Single charge window width in Da (integer)" />
593 <param name="omssa_double_window_wd" type="integer" value="14"
594 label="OMSSA: Double Charge Window Width" help="OMSSA double charge window width in Da (integer)" />
595 <param name="omssa_single_window_pk" type="integer" value="2"
596 label="OMSSA: Single Charge Window Peaks" help="Minimum number of peaks in single charge window (integer)" />
597 <param name="omssa_double_window_pk" type="integer" value="2"
598 label="OMSSA: Double Charge Window Peaks" help="Minimum number of peaks in double charge window (integer)" />
599 <param name="omssa_min_ann_int_pks" type="integer" value="6"
600 label="OMSSA: Minimum Number of Annotated Peaks of Intense Ones" help="Minimum number of annotated peaks among the most intense ones" />
601 <param name="omssa_min_annotated_peaks" type="integer" value="2"
602 label="OMSSA: Minimum number of Annotated Peaks" help="Minimum number of annotated peaks" />
603 <param name="omssa_min_peaks" type="integer" value="4"
604 label="OMSSA: Minimum Peak Count" help="The minimum number of m/z values a spectrum must have to be searched" />
605 <param name="omssa_methionine" type="boolean" truevalue="1" falsevalue="0" checked="true"
606 label="OMSSA: Cleave n-term Methionine" help="Allow for N-terminal methionine cleavage" />
607 <param name="omssa_max_ladders" type="integer" value="128"
608 label="OMSSA: Maximum Number of m/z Ladders" help="The maximum number of mass ladders to generate per database peptide" />
609 <param name="omssa_max_frag_charge" type="integer" value="2"
610 label="OMSSA: Maximum Fragment Charge" help="Maximum fragment charge" />
611 <param name="omssa_fraction" type="float" value="0.95"
612 label="OMSSA: Fraction of Peaks to estimate Charge 1" help="fraction of peaks to estimate charge 1" />
613 <param name="omssa_plus_one" type="boolean" truevalue="1" falsevalue="0" checked="true"
614 label="OMSSA: Estimate Plus One Charge" help="Allow OMSSA to estimate plus one charge algorithmically"/>
615 <param name="omssa_charge" type="select"
616 label="OMSSA: Fragment Charge" help="OMSSA fragment charge option" >
617 <option value="0" >Minus</option>
618 <option value="1" selected="True">Plus</option>
619 </param>
620 <param name="omssa_prec_per_spectrum" type="integer" value="1"
621 label="OMSSA: Minimum Number of Precursors per Spectrum" help="Minimum number of precursors per spectrum" />
622 <param name="omssa_forward" type="boolean" truevalue="1" falsevalue="0" checked="true"
623 label="OMSSA: Include First Forward Ion (b1) in Search" help="Allow OMSSA to include first forward ion (b1) in search" />
624 <param name="omssa_rewind" type="boolean" truevalue="1" falsevalue="0" checked="true"
625 label="OMSSA: Search Rewind" help="Allow search rewind (C-terminal) ions" />
626 <param name="omssa_max_frag_series" type="integer" value="100"
627 label="OMSSA: Maximum Fragment per Series" help="Max number of fragments ions ions in each series being searched" />
628 <param name="omssa_corr" type="boolean" truevalue="1" falsevalue="0" checked="true"
629 label="OMSSA: Use Correlation Correction" help="Allow the use correlation correction score" />
630 <param name="omssa_consecutive_p" type="float" value="0.5"
631 label="OMSSA: Consecutive Ion Probability" help="Probability of consecutive ion (used in correlation correction)" />
632 <param name="omssa_it_sequence_evalue" type="float" value="0.0"
633 label="OMSSA: Sequence e-value Cutoff" help="The maximum e-value allowed to consider a sequence in the iterative search(0.0 means all)" />
634 <param name="omssa_it_spectrum_evalue" type="float" value="0.01"
635 label="OMSSA: Spectrum e-value Cutoff" help="The maximum e-value allowed to consider a spectrum in the iterative search(0.0 means all)" />
636 <param name="omssa_it_replace_evalue" type="float" value="0.01"
637 label="OMSSA: Replace e-value cutoff" help="The maximum e-value allowed to replace a hit in the iterative search(0.0 means all)" />
638 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
639 label="OMSSA: Remove Precursor" help="Remove precursors" />
640 <param name="omssa_scale_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
641 label="OMSSA: Scale Precursor Mass" help="scale precursor mass" />
642 <param name="omssa_estimate_charge" type="boolean" truevalue="1" falsevalue="0" checked="true"
643 label="OMSSA: Remove Precursor" help="Remove precursors" />
644 <param name="omssa_max_evalue" type="float" value="100"
645 label="OMSSA: Maximal evalue Considered" help="The maximum e-value considered" />
646 <param name="omssa_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="true"
647 label="OMSSA: Estimate Precursor Charge" help="Allow estimation of precursor charge" />
648 <param name="omssa_it_replace_evalue" type="float" value="100"
649 label="OMSSA: Maximal evalue" help="The maximum OMSSA e-value considered" />
650 <param name="omssa_hitlist_length" type="integer" value="0"
651 label="OMSSA: Hitlist Length" help="OMSSA hitlist length, 0 means all" />
652 <param name="omssa_hitlist_charge" type="integer" value="30"
653 label="OMSSA: Number of Hits per Spectrum per Charge" help="number of hits per spectrum per charge" />
654 <param name="omssa_min_pep_length" type="integer" value="4"
655 label="OMSSA: Minumum Peptide Length" help="Minimum length of peptides for no-enzyme and semi-tryptic searches" />
656 <param name="omssa_max_pep_length" type="integer" value="40"
657 label="OMSSA: Maximum Peptide Length" help="Maximum length of peptides for no-enzyme and semi-tryptic searches (0: none)" />
658 <param name="omssa_format" label="OMSSA output format" type="select" >
659 <option value="0" selected="True">OMX</option>
660 <option value="1" >CSV</option>
661 </param>
662 </when>
663 </conditional>
664
665 <!-- MS-GF+ ADVANCED PARAMETERS -->
666 <conditional name="msgf">
667 <param name="msgf_advanced" type="select" label="MSGF Options">
668 <option value="yes">Advanced</option>
669 <option value="no" selected="True">Default</option>
670 </param>
671 <when value="no" />
672 <when value="yes">
673 <param name="msgf_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
674 label="MSGF: Search Decoys" help="If yes then a decoy database will be generated and searched. Assumed input database contains no decoys"/>
675 <param name="msgf_min_pep_length" type="integer" value="6"
676 label="MSGF: Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
677 <param name="msgf_max_pep_length" type="integer" value="30"
678 label="MSGF: Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
679 <param name="msgf_termini" type="select" format="txt"
680 label="MSGF: Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
681 <option value="0">0 (ie non-specific cleavage)</option>
682 <option value="1">1 (ie semi-tryptic cleavage)</option>
683 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
684 </param>
685 <param name="msgf_num_ptms" label="MSGF: Max PTMs per peptide" type="integer" value="2"/>
686
687 <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)">
688 <option value="0" selected="True">Low-res LCQ/LTQ</option>
689 <option value="1" >High-res LTQ</option>
690 <option value="2" >TOF</option>
691 <option value="3" >Q-Exactive</option>
692 </param>
693 <param name="msgf_fragmentation" label="MSGF: Fragmentation type" type="select" help="Fragmentation method identifier (used to determine the scoring model)">
694 <option value="0" selected="True">As written in the spectrum or CID if no info</option>
695 <option value="1" >CID</option>
696 <option value="2" >ETD</option>
697 <option value="3" >HCD</option>
698 </param>
699 <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">
700 <option value="0" selected="True">Automatic</option>
701 <option value="1" >Phosphorylation</option>
702 <option value="2" >iTRAQ</option>
703 <option value="3" >iTRAQPhospho</option>
704 <option value="4" >TMT</option>
705 <option value="5" >Standard</option>
706 </param>
707 <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" />
708 <param name="msgf_additional" label="MS-GF+ additional features" type="select" help="Additional features to export">
709 <option value="0" selected="True">output basic scores only</option>
710 <option value="1" >output additional features</option>
711 </param>
712 </when>
713 </conditional>
714
715 <!-- MS-AMANDA ADVANCED PARAMETERS -->
716 <conditional name="ms_amanda">
717 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
718 <option value="yes">Advanced</option>
719 <option value="no" selected="True">Default</option>
720 </param>
721 <when value="no" />
722 <when value="yes">
723 <param name="ms_amanda_decoy" type="boolean" truevalue="1" falsevalue="0" checked="false"
724 label="MS Amanda: Generate Decoys" help="generate decoys" />
725 <param name="ms_amanda_instrument" label="MS Amanda: instrument" type="select"
726 help="MS Amanda instrument id option. Available ion types are listed here.">
727
728 <option value="b, y" selected="True">b, y</option>
729 <option value="b, y, -H2O, -NH3" >b, y, -H2O, -NH3</option>
730 <option value="a, b, y, -H2O, -NH3, Imm" >a, b, y, -H2O, -NH3, Imm</option>
731 <option value="a, b, y, -H2O, -NH3" >a, b, y, -H2O, -NH3</option>
732 <option value="a, b, y" >a, b, y</option>
733 <option value="a, b, y, Imm" >a, b, y, Imm</option>
734 <option value="a, b, y, z, -H2O, -NH3, Imm" >a, b, y, z, -H2O, -NH3, Imm</option>
735 <option value="c, y, z+1, z+2" >c, y, z+1, z+2</option>
736 <option value="b, c, y, z+1, z+2" >b, c, y, z+1, z+2</option>
737 <option value="b, y, INT" >b, y, INT</option>
738 <option value="b, y, INT, Imm" >b, y, INT, Imm</option>
739 <option value="a, b, y, INT" >a, b, y, INT</option>
740 <option value="a, b, y, INT, IMM" >a, b, y, INT, IMM</option>
741 <option value="a, b, y, INT, IMM, -H2O" >a, b, y, INT, IMM, -H2O</option>
742 <option value="a, b, y, INT, IMM, -H2O, -NH3" >a, b, y, INT, IMM, -H2O, -NH3</option>
743 <option value="a, b, y, INT, IMM, -NH3" >a, b, y, INT, IMM, -NH3</option>
744
745 </param>
746 <param name="ms_amanda_max_rank" type="integer" value="10"
747 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
748 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
749 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
750 </when>
751 </conditional>
752
753
754 <!-- TIDE ADVANCED PARAMETERS -->
755 <conditional name="tide">
756 <param name="tide_advanced" type="select" label="TIDE Options">
757 <option value="yes">Advanced</option>
758 <option value="no" selected="True">Default</option>
759 </param>
760 <when value="no" />
761 <when value="yes">
762 <param name="tide_num_ptms" type="integer" value="" optional="true"
763 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/>
764 <param name="tide_num_ptms_per_type" type="integer" value="2"
765 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/>
766 <param name="tide_min_pep_length" type="integer" value="6"
767 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/>
768 <param name="tide_max_pep_length" type="integer" value="30"
769 label="TIDE: Maximum Peptide Length" help="Set the maximum length of peptide to be considered"/>
770 <param name="tide_min_prec_mass" type="float" value="200.0"
771 label="TIDE: Minimum Precursor Mass" help="Set the minimum precursor mass to be considered"/>
772 <param name="tide_max_prec_mass" type="float" value="7200.0"
773 label="TIDE: Maximum Precursor Mass" help="Set the maximum precursor mass to be considered"/>
774 <param name="tide_decoy_format" label="TIDE: Decoy Format" type="select" help="Select the format for generating the decoy sequences">
775 <option value="none" selected="True">none</option>
776 <option value="shuffle" >shuffle</option>
777 <option value="peptide-revers" >peptide-reverse</option>
778 <option value="protein-reverse" >protein-reverse</option>
779 </param>
780 <param name="tide_keep_terminals" label="TIDE: Keep Terminals" type="select" help="Select to keep the terminal amino acids when creating decoys">
781 <option value="N" >N</option>
782 <option value="C" >C</option>
783 <option value="NC" selected="True">NC</option>
784 <option value="non" >none</option>
785 </param>
786 <param name="tide_decoy_seed" type="integer" value="1"
787 label="TIDE: Decoy Seed" help="Set the decoy seed"/>
788 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false"
789 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/>
790 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress">
791 <option value="0" >0</option>
792 <option value="10" >10</option>
793 <option value="20" >20</option>
794 <option value="30" selected="True">30</option>
795 <option value="40" >40</option>
796 <option value="50" >50</option>
797 <option value="60" >60</option>
798 </param>
799
800 <param name="tide_monoisotopic" type="boolean" truevalue="1" falsevalue="0" checked="true"
801 label="TIDE: Monoisotopic" help="If true, the precursor mass is monoisotopic"/>
802 <param name="tide_clip_n_term" type="boolean" truevalue="1" falsevalue="0" checked="false"
803 label="TIDE: Clip Nterm Methionine" help="If true, the Nterm Methionine will be clipped"/>
804 <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">
805 <option value="full-digest" selected="True">full-digest</option>
806 <option value="partial-digest" >partial-digest</option>
807 </param>
808 <param name="tide_compute_sp" type="boolean" truevalue="1" falsevalue="0" checked="false"
809 label="TIDE: Compute SP" help="If true, the SP-score is calculated"/>
810 <param name="tide_max_psms" type="integer" value="10"
811 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/>
812 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false"
813 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/>
814 <param name="tide_min_spectrum_mz" type="float" value="0.0"
815 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/>
816 <param name="tide_max_spectrum_mz" type="float" value="" optional="true"
817 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/>
818 <param name="tide_min_spectrum_peaks" type="integer" value="20"
819 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/>
820 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching">
821 <option value="1" >1</option>
822 <option value="2" >2</option>
823 <option value="3" >3</option>
824 <option value="all" selected="True">all</option>
825 </param>
826 <param name="tide_remove_prec" type="boolean" truevalue="1" falsevalue="0" checked="false"
827 label="TIDE: Remove Precursor" help="If true, the peak that corresponds to the precursor mass is excluded"/>
828 <param name="tide_remove_prec_tol" type="float" value="1.5"
829 label="TIDE: Remove Precursor Tolerance" help="Choose the threshold for precursor mass searching (for precursor peak removal)"/>
830 <param name="tide_progress_indicator" type="integer" value="1000"
831 label="TIDE: Progress Indicator" help="Choose the progress indicator frequency (in number of fragmentation spectra processed)"/>
832 <param name="tide_use_flanking" type="boolean" truevalue="1" falsevalue="0" checked="false"
833 label="TIDE: Use Flanking" help="Includes two flanking peaks on either side of each b- and y-ion to compute the XCorr"/>
834 <param name="tide_use_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="false"
835 label="TIDE: Neutral Losses" help="Includes fragment peaks with neutral losses to perform the matching"/>
836 <param name="tide_mz_bin_width" type="float" value="0.02"
837 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/>
838 <param name="tide_mz_bin_offset" type="float" value="0.0"
839 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/>
840 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false"
841 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/>
842
843 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format">
844 <option value="tide_export_text" selected="True">Text</option>
845 <option value="tide_export_sqt" >SQT</option>
846 <option value="tide_export_pepxml" >pepxml</option>
847 <option value="tide_export_mzid" >MzIdentML</option>
848 <option value="tide_export_pin" >Percolator input file</option>
849 </param>
850
851 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
852 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
853 </when>
854 </conditional>
855
856
857 <!-- MyriMatch ADVANCED PARAMETERS -->
858 <conditional name="myrimatch">
859 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
860 <option value="yes">Advanced</option>
861 <option value="no" selected="True">Default</option>
862 </param>
863 <when value="no" />
864 <when value="yes">
865 <param name="myrimatch_min_pep_length" type="integer" value="8"
866 label="MyriMatch: Minimum Peptide Length" help="Minimum length for a peptide to be considered" />
867 <param name="myrimatch_max_pep_length" type="integer" value="30"
868 label="MyriMatch: Maximum Peptide Length" help="Maximum length for a peptide to be considered" />
869 <param name="myrimatch_min_prec_mass" type="float" value="600.0"
870 label="MyriMatch: Minimum Precursor Mass" help="Minimum precursor mass of parent ion to be considered" />
871 <param name="myrimatch_max_prec_mass" type="float" value="5000.0"
872 label="MyriMatch: Maximum Precursor Mass" help="Maximum precursor mass of parent ion to be considered" />
873 <param name="myrimatch_num_matches" type="integer" value="10"
874 label="MyriMatch: Maximum Number of Spectrum Matches" help="Set the value for the maximum number of spectrum matches" />
875 <param name="myrimatch_num_ptms" type="integer" value="2"
876 label="MyriMatch: Max Variable PTMs per Peptide" help="Set the number of PTMS allowed per peptide" />
877 <param name="myrimatch_fragmentation" label="MyriMatch: Fragmentation Method" type="select" help="Choose the fragmentation method used (CID: b,y) or (ETD: c, z*)">
878 <option value="CID" selected="True">CID</option>
879 <option value="HCD" >HCD</option>
880 <option value="ETD" >ETD</option>
881 </param>
882 <param name="myrimatch_termini" label="MyriMatch: Enzymatic Terminals" type="select" help="Select the number of enzymatic terminals">
883 <option value="0">None required</option>
884 <option value="1">At least one</option>
885 <option value="2" selected="True" >Both</option>
886 </param>
887 <param name="myrimatch_plus_three" type="boolean" truevalue="1" falsevalue="0" checked="true"
888 label="MyriMatch: Use Smart Plus Three Option" help="Defines what algorithms are used to generate a set of theoretical fragment ions" />
889 <param name="myrimatch_xcorr" type="boolean" truevalue="1" falsevalue="0" checked="false"
890 label="MyriMatch: Compute Xcorr" help="a Sequest-like cross correlation score can be calculated for the top ranking hits" />
891 <param name="myrimatch_tic_cutoff" type="float" value="0.98"
892 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)" />
893 <param name="myrimatch_intensity_classes" type="integer" value="3"
894 label="MyriMatch: Number of Intensity Classes" help="Experimental spectra have their peaks stratified into this number of intensity classed" />
895 <param name="myrimatch_class_multiplier" type="integer" value="2"
896 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" />
897 <param name="myrimatch_num_batches" type="integer" value="50"
898 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
899 <param name="myrimatch_max_peak" type="integer" value="100"
900 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
901 </when>
902 </conditional>
903
904
905 <!-- Andromeda ADVANCED PARAMETERS -->
906 <!-- Windows only
907 <conditional name="andromeda">
908 <param name="andromeda_advanced" type="select" label="Andromeda Options">
909 <option value="yes">Advanced</option>
910 <option value="no" selected="True">Default</option>
911 </param>
912 <when value="no" />
913 <when value="yes">
914 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" />
915 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" />
916 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" />
917 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" />
918 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" />
919 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" />
920 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" />
921 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" />
922 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" />
923 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" />
924 <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" />
925 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." >
926 <option value="CID" selected="true">CID</option>
927 <option value="HCD">HCD</option>
928 <option value="EDT">EDT</option>
929 </param>
930 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" />
931 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" />
932 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" />
933 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" />
934 <param name="andromeda_decoy_mode" type="boolean" truevalue="decoy" falsevalue="none" checked="false" label="Andromeda decoy mode" />
935 </when>
936 </conditional>
937 -->
938
939 <!-- Comet ADVANCED PARAMETERS -->
940 <conditional name="comet">
941 <param name="comet_advanced" type="select" label="Comet Options">
942 <option value="yes">Advanced</option>
943 <option value="no" selected="True">Default</option>
944 </param>
945 <when value="no" />
946 <when value="yes">
947 <!-- Spectrum Related parameters -->
948 <conditional name="comet_spectrum">
949 <param name="comet_spectrum_selector" type="select" label="Comet: Spectrum Related">
950 <option value="yes">Set Spectrum Parameters</option>
951 <option value="no" selected="True">Keep Default Spectrum Parameters</option>
952 </param>
953 <when value="no" />
954 <when value="yes">
955 <param name="comet_min_peaks" type="integer" value="10"
956 label="Comet: Minimum Number of Peaks per Spectrum" help="The minimum number of peaks per spectrum" />
957 <param name="comet_min_peak_int" type="float" value="0.0"
958 label="Comet: Minimum Peaks Intensity" help="The minimum intensity for input peaks to be considered" />
959 <conditional name="comet_prec">
960 <param name="comet_remove_prec" label="Comet: Remove Precursor" type="select" help="Select for precursor m/z signal removal">
961 <option value="0" selected="True" >off</option>
962 <option value="1">on</option>
963 <option value="2">as expected for ETD/ECD spectra</option>
964 </param>
965 <when value="0" />
966 <when value="1">
967 <param name="comet_remove_prec_tol" type="float" value="1.5"
968 label="Comet: Remove Precursor Tolerance" />
969 </when>
970 <when value="2">
971 <param name="comet_remove_prec_tol" type="float" value="1.5"
972 label="Comet: Remove Precursor Tolerance" />
973 </when>
974 </conditional>
975 <param name="comet_clear_mz_range_lower" type="float" value="0.0"
976 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" />
977 <param name="comet_clear_mz_range_upper" type="float" value="0.0"
978 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" />
979 </when>
980 </conditional>
981 <!-- Search Related parameters -->
982 <conditional name="comet_search">
983 <param name="comet_search_selector" type="select" label="Comet: Search Related">
984 <option value="yes">Set Search Parameters</option>
985 <option value="no" selected="True">Keep Default Search Parameters</option>
986 </param>
987 <when value="no" />
988 <when value="yes">
989 <param name="comet_enzyme_type" label="Comet: Enzyme Type" type="select" help="Specifies the number of enzyme termini a peptide must have">
990 <option value="1">semi-specific</option>
991 <option value="2" selected="True">full-enzyme</option>
992 <option value="8">unspecific N-term</option>
993 <option value="9">unspecific C-term</option>
994 </param>
995 <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">
996 <option value="0" selected="True">off</option>
997 <option value="1">-1,0,+1,+2,+3</option>
998 <option value="2">-8,-4,0,+4,+8</option>
999 </param>
1000 <param name="comet_min_prec_mass" type="float" value="0.0"
1001 label="Comet: Minimum Precursor Mass" help="The minimum precursor mass considered" />
1002 <param name="comet_max_prec_mass" type="float" value="10000.0"
1003 label="Comet: Maximum Precursor Mass" help="The maximum precursor mass considered" />
1004 <param name="comet_num_matches" type="integer" value="10"
1005 label="Comet: Maximum Number of Matches" help="The maximum number of peptide matches per spectrum" />
1006 <param name="comet_max_frag_charge" type="integer" value="3"
1007 label="Comet: Maximum Fragment Charge" help="Sets the maximum fragment charge (fill value between 1 and 5)" />
1008 <param name="comet_remove_meth" type="boolean" truevalue="1" falsevalue="0" checked="false"
1009 label="Comet: Remove Methionine" help="Specifies whether the N-terminal methionine is cleaved prior to matching" />
1010 <param name="comet_batch_size" type="integer" value="0"
1011 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" />
1012 <param name="comet_num_ptms" type="integer" value="10"
1013 label="Comet: Maximum Number of PTMs" help="The maximum number of ptms per peptide" />
1014 </when>
1015 </conditional>
1016 <!-- Fragment Ions Related parameters -->
1017 <conditional name="comet_fragment_ions">
1018 <param name="comet_fragment_ions_selector" type="select" label="Comet: Fragment Ions Related">
1019 <option value="yes">Set Fragment Ions Parameters</option>
1020 <option value="no" selected="True">Keep Default Fragment Ions Parameters</option>
1021 </param>
1022 <when value="no" />
1023 <when value="yes">
1024 <param name="comet_frag_bin_offset" type="float" value="0.4"
1025 label="Comet: Fragment Bin Offset" help="Controls how each fragment bin is defined in terms of where each bin starts" />
1026 <param name="comet_theoretical_fragment_ions" type="integer" value="0"
1027 label="Comet: Theoretical Fragment Ions" help="Specifies how theoretical fragment ion peaks are represented (0 or 1 values are allowed)" />
1028 </when>
1029 </conditional>
1030 </when>
1031 </conditional>
1032 <conditional name="directtag">
1033 <param name="directtag_advanced" type="select" label="DirectTag Options">
1034 <option value="yes">Advanced</option>
1035 <option value="no" selected="True">Default</option>
1036 </param>
1037 <when value="no" />
1038 <when value="yes">
1039 <param name="directag_tic_cutoff" type="integer" value="85" label="DirecTag TIC cutoff in percent, default is '85'."/>
1040 <param name="directag_max_peak_count" type="integer" value="400" label="DirecTag max peak count, default is '400'."/>
1041 <param name="directag_intensity_classes" type="integer" value="3" label="DirecTag number of intensity classses, default is '3'."/>
1042 <param name="directag_adjust_precursor" type="boolean" truevalue="1" falsevalue="0" checked="false" label="DirecTag adjust precursor, default is false."/>
1043 <param name="directag_min_adjustment" type="float" value="-2.5" label="DirecTag minimum precursor adjustment, default is '-2.5'."/>
1044 <param name="directag_max_adjustment" type="float" value="2.5" label="DirecTag maximum precursor adjustment, default is '2.5'."/>
1045 <param name="directag_adjustment_step" type="float" value="0.1" label="DirecTag precursor adjustment step, default is '0.1'."/>
1046 <param name="directag_charge_states" type="integer" value="3" label="DirecTag number of charge states considered, default is '3'."/>
1047 <param name="directag_output_suffix" type="text" value="" label="DirecTag output suffix, default is no suffix."/>
1048 <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."/>
1049 <param name="directag_duplicate_spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" label="DirecTag duplicate spectra per charge, default is true."/>
1050 <param name="directag_deisotoping" type="select" label="DirecTag deisotoping mode, default is no deisotoping">
1051 <option value="0" selected="true">no deisotoping</option>
1052 <option value="1">precursor only</option>
1053 <option value="2">precursor and candidate</option>
1054 </param>
1055 <param name="directag_isotope_tolerance" type="float" value="0.25" label="DirecTag isotope mz tolerance, default is '0.25'."/>
1056 <param name="directag_complement_tolerance" type="float" value="0.5" label="DirecTag complement mz tolerance, default is '0.5'."/>
1057 <param name="directag_tag_length" type="integer" value="3" label="DirecTag tag length, default is '3'."/>
1058 <param name="directag_max_var_mods" type="integer" value="2" label="DirecTag maximum variable modifications per sequence, default is '2'."/>
1059 <param name="directag_max_tag_count" type="integer" value="20" label="DirecTag maximum tag count, default is '20'."/>
1060 <param name="directag_intensity_weight" type="float" value="1.0" label="DirecTag intensity score weight, default is '1.0'."/>
1061 <param name="directag_fidelity_weight" type="float" value="1.0" label="DirecTag fidelity score weight, default is '1.0'."/>
1062 <param name="directag_complement_weight" type="float" value="1.0" label="DirecTag complement_score_weight, default is '1.0'."/>
1063 </when>
1064 </conditional>
1065
1066 <conditional name="novor">
1067 <param name="novor_advanced" type="select" label="Novor Options">
1068 <option value="yes">Advanced</option>
1069 <option value="no" selected="True">Default</option>
1070 </param>
1071 <when value="no" />
1072 <when value="yes">
1073 <param name="novor_fragmentation" type="select" label="Novor fragmentation method">
1074 <option value="HCD" selected="True">HCD</option>
1075 <option value="CID">CID</option>
1076 </param>
1077 <param name="novor_mass_analyzer" label="Novor: mass analyzer" type="select" help="Identifier of the instrument to generate MS/MS spectra">
1078 <option value="FT" selected="True">FT</option>
1079 <option value="Trap" >Trap</option>
1080 <option value="TOF" >TOF</option>
1081 </param>
1082 </when>
1083 </conditional>
1084 </section>
224 </inputs> 1085 </inputs>
225 <outputs> 1086 <outputs>
226 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" /> 1087 <data name="searchgui_results" format="searchgui_archive" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
227 </outputs> 1088 </outputs>
228 <tests> 1089 <tests>
229 1090
230 <!-- Test that specifying non-default search engines works --> 1091 <!-- Test that specifying non-default search engines works -->
231 <test> 1092 <test>
232 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/> 1093 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
233 <!-- <param name="input_par" value="Identification_Parameters_specific.par"/>--> 1094 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
234 <param name="input_zip" value="IdentificationParametersAndFastaSpecific.zip" ftype="zip" /> 1095 <param name="precursor_ion_tol" value="100"/>
1096 <param name="min_charge" value="1"/>
1097 <param name="max_charge" value="3"/>
235 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/> 1098 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1099 <param name="xtandem.xtandem_advanced" value="yes"/>
1100 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
236 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" /> 1101 <output name="searchgui_results" file="tiny_searchgui_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
237 </test> 1102 </test>
238 <!-- Test that search works with MSAmanda --> 1103 <!-- Test that search works with MSAmanda -->
239 <test> 1104 <test>
240 <param name="peak_lists" value="searchgui_smallspectra.mgf"/> 1105 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
241 <!-- <param name="input_par" value="Identification_Parameters_default.par"/>--> 1106 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
242 <param name="input_zip" value="IdentificationParametersAndFastaDefault.zip" ftype="zip" /> 1107 <param name="precursor_ion_tol" value="100"/>
1108 <param name="min_charge" value="1"/>
1109 <param name="max_charge" value="3"/>
243 <param name="engines" value="MS_Amanda"/> 1110 <param name="engines" value="MS_Amanda"/>
244 <output name="searchgui_results" file="smallsearch_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" /> 1111 <output name="searchgui_results" file="tiny_searchgui_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
245 </test> 1112 </test>
246 1113
1114 <!-- Test that specifying non-default search engines works using modifications -->
1115 <!--
1116 <test>
1117 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1118 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1119 <param name="precursor_ion_tol" value="100"/>
1120 <param name="fixed_modifications" value="carbamidomethyl c"/>
1121 <param name="variable_modifications" value="oxidation of m"/>
1122 <param name="min_charge" value="1"/>
1123 <param name="max_charge" value="3"/>
1124 <param name="engines" value="X!Tandem,MSGF,MyriMatch,OMSSA,Comet"/>
1125 <param name="xtandem.xtandem_advanced" value="yes"/>
1126 <param name="xtandem_advanced.xtandem_refine_selector" value="yes"/>
1127 <output name="searchgui_results" file="tiny_searchgui_modifications_result1.zip" ftype="searchgui_archive" compare="sim_size" delta="30000" />
1128 </test>
1129 -->
1130 <!-- Test that search works with MSAmanda - with modifications -->
1131 <!--
1132 <test>
1133 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
1134 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
1135 <param name="precursor_ion_tol" value="100"/>
1136 <param name="fixed_modifications" value="carbamidomethyl c"/>
1137 <param name="variable_modifications" value="oxidation of m"/>
1138 <param name="min_charge" value="1"/>
1139 <param name="max_charge" value="3"/>
1140 <param name="engines" value="MS_Amanda"/>
1141 <output name="searchgui_results" file="tiny_searchgui_modifications_result_amandaonly.zip" ftype="searchgui_archive" compare="sim_size" delta="5000" />
1142 </test>
1143 -->
247 </tests> 1144 </tests>
248 <help> 1145 <help>
249 **What it does** 1146 **What it does**
250 1147
251 Runs multiple search engines on any number of MGF peak lists using the SearchGUI. 1148 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
252
253 Default: X! Tandem, OMSSA and MS-GF+ are executed. 1149 Default: X! Tandem, OMSSA and MS-GF+ are executed.
254
255 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed. 1150 Optional: MyriMatch, MS-Amanda, Comet and Tide can be executed.
256 1151
257 </help> 1152 </help>
258 <expand macro="citations" /> 1153 <expand macro="citations" />
259 </tool> 1154 </tool>