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comparison searchgui.xml @ 20:2cafc729b2ae draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0e976aeeed9d516e0ad4735dc847b1f2eba3532b
author iracooke
date Sun, 31 May 2015 09:05:57 -0400
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children dfaea053e32f
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19:7e61179c5952 20:2cafc729b2ae
1 <tool id="search_gui" name="Search GUI" version="1.27.0">
2 <description>
3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
4 </description>
5 <requirements>
6 <requirement type="package" version="1.27">searchgui</requirement>
7 </requirements>
8 <macros>
9 <import>macros.xml</import>
10 </macros>
11 <expand macro="stdio" />
12 <command>
13 <![CDATA[
14 #from datetime import datetime
15 #set $exp_str = "Galaxy_Experiment_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
16 #set $samp_str = "Sample_%s" % datetime.now().strftime("%Y%m%d%H%M%s")
17 #set $temp_stderr = "searchgui_stderr"
18
19 mkdir output;
20 mkdir output_reports;
21 cwd=`pwd`;
22 #for $mgf in $peak_lists:
23 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
24 ln -s -f '${mgf}' '${input_name}';
25 #end for
26 ##ln -s "${input_database}" input_database.fasta;
27 cp "${input_database}" input_database.fasta;
28
29 ###########################################
30 #### Creating decoy database ####
31 ###########################################
32 #if $create_decoy:
33 echo "Creating decoy database.";
34 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
35 rm input_database.fasta &&
36 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
37 ##ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
38 #end if
39
40 #####################################################
41 ## generate IdentificationParameters for SearchGUI ##
42 #####################################################
43
44 (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI
45 -out SEARCHGUI_IdentificationParameters.parameters
46
47 @GENERAL_PARAMETERS@
48
49 -db input_database.fasta
50
51 #if $advanced.advanced_type_selector == "advanced":
52
53 #if $advanced.xtandem.xtandem_selector == "yes"
54
55 -xtandem_npeaks ${advanced.xtandem.xtandem_npeaks}
56 -xtandem_min_peaks ${advanced.xtandem.xtandem_min_peaks}
57 -xtandem_min_frag_mz ${advanced.xtandem.xtandem_min_frag_mz}
58 -xtandem_min_prec_mass ${advanced.xtandem.xtandem_min_prec_mass}
59 -xtandem_noise_suppr ${advanced.xtandem.xtandem_noise_suppr}
60
61 #if $advanced.xtandem.xtandem_refine.xtandem_refine_selector == "yes"
62 -xtandem_refine 1
63 -xtandem_refine_unc ${advanced.xtandem.xtandem_refine.xtandem_refine_unc}
64 -xtandem_refine_semi ${advanced.xtandem.xtandem_refine.xtandem_refine_semi}
65 -xtandem_refine_p_mut ${advanced.xtandem.xtandem_refine.xtandem_refine_p_mut}
66 -xtandem_refine_snaps ${advanced.xtandem.xtandem_refine.xtandem_refine_snaps}
67 -xtandem_refine_spec_synt ${advanced.xtandem.xtandem_refine.xtandem_refine_spec_synt}
68 #end if
69 #end if
70
71 #if $advanced.omssa.omssa_selector == "yes"
72 -omssa_hitlist_length ${advanced.omssa.hitlist_length}
73 -omssa_remove_prec ${advanced.omssa.remove_precursor}
74 -omssa_scale_prec ${advanced.omssa.scale_precursor}
75 -omssa_estimate_charge ${advanced.omssa.estimate_charge}
76 #end if
77
78 #if $advanced.msgf.msgf_selector == "yes"
79 -msgf_min_pep_length ${advanced.msgf.msgf_min_pep_length}
80 -msgf_max_pep_length ${advanced.msgf.msgf_max_pep_length}
81 -msgf_termini ${advanced.msgf.msgf_termini}
82 -msgf_num_ptms ${advanced.msgf.msgf_num_ptms}
83 #end if
84
85 ##if $advanced.ms_amanda.ms_amanda_selector == "yes"
86 ##end if
87
88 #end if
89
90 2> $temp_stderr)
91 &&
92
93 ################
94 ## Search CLI ##
95 ################
96 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI
97 -temp_folder `pwd`
98 -spectrum_files \$cwd
99 -output_folder \$cwd/output
100 -id_params SEARCHGUI_IdentificationParameters.parameters
101
102 -threads "\${GALAXY_SLOTS:-12}"
103 -correct_titles "${correct_titles}"
104 $missing_titles
105 -mgf_splitting "${mgf_splitting}"
106 -mgf_spectrum_count "${mgf_spectrum_count}"
107
108 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
109 ## the tree is generated afterwards in PeptideShaker
110 -protein_index 0
111
112 ##-makeblastdb_folder \$BLAST_ROOT_DIR
113
114 #if $advanced.advanced_type_selector == "advanced":
115
116 #if $advanced.xtandem.xtandem_selector == "yes"
117 -xtandem 1
118 #else
119 -xtandem 0
120 #end if
121
122 #if $advanced.omssa.omssa_selector == "yes"
123 -omssa 1
124 #else
125 -omssa 0
126 #end if
127
128 #if $advanced.msgf.msgf_selector == "yes"
129 -msgf 1
130 #else
131 -msgf 0
132 #end if
133
134 #if $advanced.myrimatch.myrimatch_selector == "yes"
135 -myrimatch 1
136 #else
137 -myrimatch 0
138 #end if
139
140 #if $advanced.comet.comet_selector == "yes"
141 -comet 1
142 #else
143 -comet 0
144 #end if
145
146 #if $advanced.ms_amanda.ms_amanda_selector == "yes"
147 -ms_amanda 1
148 #else
149 -ms_amanda 0
150 #end if
151
152 #if $advanced.tide.tide_selector == "yes"
153 -tide 1
154 #else
155 -tide 0
156 #end if
157
158 #else
159 -ms_amanda 0 -tide 0
160 #end if
161
162 ## single zip file
163 -output_option 0
164
165 ## mgf and database in output
166 -output_data 1
167
168 2>> $temp_stderr)
169
170 &&
171
172 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
173
174 &&
175
176 exit_code_for_galaxy=\$?;
177 cat $temp_stderr 2>&1;
178 (exit \$exit_code_for_galaxy)
179 ]]>
180 </command>
181 <inputs>
182 <param format="fasta" name="input_database" type="data" label="Protein Database"
183 help="Select FASTA database from history"/>
184
185 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
186 label="Create a concatenated target/decoy database before running PeptideShaker"
187 help="Selecting this option will help PeptideShaker calculate FDR values" />
188
189 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
190 help="Select appropriate MGF dataset(s) from history" />
191
192 <expand macro="general_options"/>
193
194 <param name="correct_titles" type="select" label="How should PeptideShaker deal with duplicate spectra?"
195 help="Unless you suspect some input files to be genuine duplicates then rename spectra is the safest option">
196 <option value="0">no correction</option>
197 <option value="1" selected="True">rename spectra</option>
198 <option value="2">delete spectra</option>
199 </param>
200
201 <param name="missing_titles" type="boolean" checked="false" truevalue="-missing_titles 1" falsevalue="-missing_titles 0"
202 label="Add missing spectrum titles" help="(-missing_titles)"/>
203
204 <param name="mgf_splitting" type="integer" value="1000" label="The maximum mgf file size in MB before splitting the mgf"
205 help="Choose a smaller value if you are running on a machine with limited memory"/>
206
207 <param name="mgf_spectrum_count" type="integer" value="25000" label="The maximum number of spectra per mgf file when splitting"
208 help="Choose a smaller value if you are running on a machine with limited memory"/>
209
210 <conditional name="advanced">
211 <param name="advanced_type_selector" type="select" label="Basic or Advanced Search options">
212 <option value="basic" selected="True">Basic</option>
213 <option value="advanced">Advanced</option>
214 </param>
215 <when value="basic" />
216 <when value="advanced">
217 <conditional name="xtandem">
218 <param name="xtandem_selector" type="select" label="Run X!Tandem search">
219 <option value="yes" selected="True">Search with X!Tandem</option>
220 <option value="no">No X!Tandem search</option>
221 </param>
222 <when value="no" />
223 <when value="yes">
224 <param name="xtandem_npeaks" type="integer" value="50"
225 label="X!Tandem: Total Peaks" help="Maximum number of peaks to be used from a spectrum"/>
226 <param name="xtandem_min_peaks" type="integer" value="15"
227 label="X!Tandem: Min Peaks" help="Minimum number of peaks required for a spectrum to be considered"/>
228 <param name="xtandem_min_frag_mz" type="integer" value="200"
229 label="X!Tandem: Min Frag m/z" help="Fragment mass peaks with m/z less than this value will be discarded"/>
230 <param name="xtandem_min_prec_mass" type="integer" value="200"
231 label="X!Tandem: Min Precursor Mass" help="Minimum mass of 1+ mass of parent ion to be considered"/>
232 <param name="xtandem_noise_suppr" type="boolean" checked="true" truevalue="1" falsevalue="0"
233 label="X!Tandem: Noise Suppression" help="Use noise suppression"/>
234
235 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
236 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
237 <option value="no" selected="True">Don't refine</option>
238 <option value="yes" >Use refinement</option>
239 </param>
240 <when value="no"/>
241 <when value="yes">
242 <param name="xtandem_refine_unc" type="boolean" truevalue="1" falsevalue="0"
243 label="X!Tandem: Unanticipated cleavage, refinement" help="Allow for unanticipated cleavage during refinement"/>
244 <param name="xtandem_refine_semi" type="boolean" truevalue="1" falsevalue="0"
245 label="X!Tandem: Cleavage semi, refinement" help="Search for semi-tryptic peptides during refinement"/>
246 <param name="xtandem_refine_p_mut" type="boolean" truevalue="1" falsevalue="0"
247 label="X!Tandem: Point mutations, refinement" help="Allow for point mutations during refinement"/>
248 <param name="xtandem_refine_snaps" type="boolean" truevalue="1" falsevalue="0"
249 label="X!Tandem: snAPs, refinement" help="Search for known single amino acid polymorphisms during refinement"/>
250 <param name="xtandem_refine_spec_synt" type="boolean" truevalue="1" falsevalue="0"
251 label="X!Tandem: Spectrum synthesis, refinement" help="Use spectrum synthesis scoring"/>
252 </when>
253 </conditional>
254 </when>
255 </conditional>
256
257 <conditional name="omssa">
258 <param name="omssa_selector" type="select" label="Run OMSSA search">
259 <option value="yes" selected="True">Search with OMSSA</option>
260 <option value="no">No OMSSA search</option>
261 </param>
262 <when value="no" />
263 <when value="yes">
264 <param name="hitlist_length" label="OMSSA: Hit List Length" type="integer" value="25" />
265 <param name="remove_precursor" label="OMSSA: Remove Precurosr" type="boolean" truevalue="1" falsevalue="0" checked="true"/>
266 <param name="scale_precursor" label="OMSSA: Scale Precursor Mass" type="boolean" truevalue="1" falsevalue="0" checked="false"/>
267 <param name="estimate_charge" label="OMSSA: Estimate Charge" type="boolean" truevalue="1" falsevalue="0" checked="true" />
268 </when>
269 </conditional>
270
271 <conditional name="msgf">
272 <param name="msgf_selector" type="select" label="Run MSGF search">
273 <option value="yes" selected="True">Search with MSGF</option>
274 <option value="no">No MSGF search</option>
275 </param>
276 <when value="no" />
277 <when value="yes">
278 <param name="msgf_min_pep_length" type="integer" value="6"
279 label="Minimum Peptide Length" help="Minimum length for a peptide to be considered"/>
280 <param name="msgf_max_pep_length" type="integer" value="30"
281 label="Maximum Peptide Length" help="Maximum length for a peptide to be considered"/>
282 <param name="msgf_termini" type="select" format="text"
283 label="Number of tolerable termini" help="Searches will take much longer if selecting a value other than 2">
284 <option value="0">0 (ie non-specific cleavage)</option>
285 <option value="1">1 (ie semi-tryptic cleavage)</option>
286 <option value="2" selected="true">2 (ie fully-tryptic cleavage)</option>
287 </param>
288 <param name="msgf_num_ptms" label="Max PTMs per peptide" type="integer" value="2"/>
289 </when>
290 </conditional>
291
292 <conditional name="myrimatch">
293 <param name="myrimatch_selector" type="select" label="Run MyriMatch search">
294 <option value="yes" selected="True">Search with MyriMatch</option>
295 <option value="no">No MyriMatch search</option>
296 </param>
297 <when value="no" />
298 <when value="yes">
299 </when>
300 </conditional>
301
302 <conditional name="comet">
303 <param name="comet_selector" type="select" label="Run Comet search">
304 <option value="yes" selected="True">Search with Comet</option>
305 <option value="no">No Comet search</option>
306 </param>
307 <when value="no" />
308 <when value="yes">
309 </when>
310 </conditional>
311
312 <conditional name="ms_amanda">
313 <param name="ms_amanda_selector" type="select" label="Run MS Amanda search">
314 <option value="yes">Search with MS Amanda</option>
315 <option value="no" selected="True">No MS Amanda search</option>
316 </param>
317 <when value="no" />
318 <when value="yes">
319 </when>
320 </conditional>
321
322 <conditional name="tide">
323 <param name="tide_selector" type="select" label="Run Tide search">
324 <option value="yes">Search with Tide</option>
325 <option value="no" selected="True">No Comet search</option>
326 </param>
327 <when value="no" />
328 <when value="yes">
329 </when>
330 </conditional>
331
332 </when>
333 </conditional>
334 </inputs>
335 <outputs>
336 <data name="searchgui_results" format="searchgui_zip" from_work_dir="searchgui_out.zip" label="${tool.name} on ${on_string}" />
337 </outputs>
338 <tests>
339 <test>
340 <param name="peak_lists" value="searchgui_tinyspectra1.mgf"/>
341 <param name="input_database" value="searchgui_tinydb1.fasta" ftype="fasta"/>
342 <param name="precursor_ion_tol" value="100"/>
343 <param name="fixed_modifications" value="carbamidomethyl c"/>
344 <param name="variable_modifications" value="oxidation of m"/>
345 <param name="min_charge" value="1"/>
346 <param name="max_charge" value="3"/>
347 <param name="advanced_type_selector" value="advanced"/>
348 <param name="xtandem_selector" value="yes"/>
349 <param name="xtandem_selector.xtandem_refine_selector" value="yes"/>
350 <param name="omssa_selector" value="no"/>
351 <param name="msgf_selector" value="yes"/>
352 <param name="ms_amanda_selector" value="no"/>
353 <output name="output" file="tiny_searchgui_result1.zip" ftype="searchgui_zip" compare="sim_size" delta="600" />
354 </test>
355 </tests>
356 <help>
357 **What it does**
358
359 Runs multiple search engines on any number of MGF peak lists using the SearchGUI.
360
361 By default X! Tandem, OMSSA, MS-GF+, Myrimatch and Comet are run. Optionally, Amanda and Tide engines can also be run.
362
363 </help>
364 <expand macro="citations" />
365 </tool>