Mercurial > repos > galaxyp > peptideshaker
comparison searchgui.xml @ 24:815f93bb3e1b draft
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author | galaxyp |
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date | Fri, 06 Nov 2015 15:33:34 -0500 |
parents | 913dbf2b83e0 |
children | 3ef5a7dd1a36 |
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23:913dbf2b83e0 | 24:815f93bb3e1b |
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1 <tool id="search_gui" name="Search GUI" version="1.28.0"> | 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> |
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.xml</import> |
7 </macros> | 7 </macros> |
8 <requirements> | 8 <requirements> |
9 <requirement type="package" version="1.28">searchgui</requirement> | 9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement> |
10 <environment_variable name="LC_ALL" action="set_to">C</environment_variable> | 10 <environment_variable name="LC_ALL" action="set_to">C</environment_variable> |
11 </requirements> | 11 </requirements> |
12 <expand macro="stdio" /> | 12 <expand macro="stdio" /> |
13 <command> | 13 <command> |
14 <![CDATA[ | 14 <![CDATA[ |
19 | 19 |
20 mkdir output; | 20 mkdir output; |
21 mkdir output_reports; | 21 mkdir output_reports; |
22 cwd=`pwd`; | 22 cwd=`pwd`; |
23 export HOME=\$cwd; | 23 export HOME=\$cwd; |
24 | |
25 ##Create a searchgui.properties file for the version, which will be added to the searchgui_results if not already present | |
26 echo "searchgui.version=@SEARCHGUI_VERSION@" >> searchgui.properties; | |
24 | 27 |
25 cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; | 28 cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin; |
26 tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; | 29 tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`; |
27 | 30 |
28 #for $mgf in $peak_lists: | 31 #for $mgf in $peak_lists: |
46 ##################################################### | 49 ##################################################### |
47 ## generate IdentificationParameters for SearchGUI ## | 50 ## generate IdentificationParameters for SearchGUI ## |
48 ##################################################### | 51 ##################################################### |
49 | 52 |
50 (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI | 53 (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI |
51 -out SEARCHGUI_IdentificationParameters.parameters | 54 -out SEARCHGUI_IdentificationParameters.par |
52 | 55 |
53 @GENERAL_PARAMETERS@ | 56 @GENERAL_PARAMETERS@ |
54 | 57 |
55 -db input_database.fasta | 58 -db input_database.fasta |
56 | 59 |
165 -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes} | 168 -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes} |
166 -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier} | 169 -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier} |
167 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches} | 170 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches} |
168 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} | 171 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} |
169 #end if | 172 #end if |
173 | |
174 #* | |
175 #if $andromeda.andromeda_advanced == "yes" | |
176 -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass} | |
177 -andromeda_max_comb ${andromeda.andromeda_max_comb} | |
178 -andromeda_top_peaks ${andromeda.andromeda_top_peaks} | |
179 -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window} | |
180 -andromeda_incl_water ${andromeda.andromeda_incl_water} | |
181 -andromeda_incl_ammonia ${andromeda.andromeda_incl_ammonia} | |
182 -andromeda_neutral_losses ${andromeda.andromeda_neutral_losses} | |
183 -andromeda_fragment_all ${andromeda.andromeda_fragment_all} | |
184 -andromeda_emp_correction ${andromeda.andromeda_emp_correction} | |
185 -andromeda_higher_charge ${andromeda.andromeda_higher_charge} | |
186 -andromeda_equal_il ${andromeda.andromeda_equal_il} | |
187 -andromeda_frag_method ${andromeda.andromeda_frag_method} | |
188 -andromeda_max_mods ${andromeda.andromeda_max_mods} | |
189 -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} | |
190 -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} | |
191 -andromeda_max_psms ${andromeda.andromeda_max_psms} | |
192 #end if | |
193 *# | |
170 | 194 |
171 #if $tide.tide_advanced == "yes" | 195 #if $tide.tide_advanced == "yes" |
172 -tide_num_ptms ${tide.tide_num_ptms} | 196 -tide_num_ptms ${tide.tide_num_ptms} |
173 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} | 197 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} |
174 -tide_min_pep_length ${tide.tide_min_pep_length} | 198 -tide_min_pep_length ${tide.tide_min_pep_length} |
254 ################ | 278 ################ |
255 (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI | 279 (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI |
256 -temp_folder `pwd` | 280 -temp_folder `pwd` |
257 -spectrum_files \$cwd | 281 -spectrum_files \$cwd |
258 -output_folder \$cwd/output | 282 -output_folder \$cwd/output |
259 -id_params SEARCHGUI_IdentificationParameters.parameters | 283 -id_params SEARCHGUI_IdentificationParameters.par |
260 | 284 |
261 -threads "\${GALAXY_SLOTS:-12}" | 285 -threads "\${GALAXY_SLOTS:-12}" |
262 | 286 |
263 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' | 287 #if $searchgui_advanced.searchgui_advanced_selector == 'advanced' |
264 -correct_titles "${searchgui_advanced.correct_titles}" | 288 -correct_titles "${searchgui_advanced.correct_titles}" |
314 -ms_amanda 1 | 338 -ms_amanda 1 |
315 #else | 339 #else |
316 -ms_amanda 0 | 340 -ms_amanda 0 |
317 #end if | 341 #end if |
318 | 342 |
343 #if 'Andromeda' in $engines_list: | |
344 -andromeda 1 | |
345 #else | |
346 -andromeda 0 | |
347 #end if | |
348 | |
319 ## single zip file | 349 ## single zip file |
320 -output_option 0 | 350 -output_option 0 |
321 | 351 |
322 ## mgf and database in output | 352 ## mgf and database in output |
323 -output_data 1 | 353 -output_data 1 |
325 2>> $temp_stderr) | 355 2>> $temp_stderr) |
326 | 356 |
327 && | 357 && |
328 | 358 |
329 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) | 359 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) |
360 | |
361 && | |
362 | |
363 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr) | |
330 | 364 |
331 && | 365 && |
332 | 366 |
333 exit_code_for_galaxy=\$?; | 367 exit_code_for_galaxy=\$?; |
334 cat $temp_stderr 2>&1; | 368 cat $temp_stderr 2>&1; |
355 <option value="MS_Amanda">MS_Amanda</option> | 389 <option value="MS_Amanda">MS_Amanda</option> |
356 <option value="MSGF" selected="True">MS-GF+</option> | 390 <option value="MSGF" selected="True">MS-GF+</option> |
357 <option value="OMSSA" selected="True">OMSSA</option> | 391 <option value="OMSSA" selected="True">OMSSA</option> |
358 <option value="Comet">Comet</option> | 392 <option value="Comet">Comet</option> |
359 <option value="Tide">Tide</option> | 393 <option value="Tide">Tide</option> |
394 <!-- Windows only | |
395 <option value="Andromeda">Andromeda</option> | |
396 --> | |
360 <validator type="no_options" message="Please select at least one output file" /> | 397 <validator type="no_options" message="Please select at least one output file" /> |
361 </param> | 398 </param> |
362 | 399 |
363 | 400 |
364 <!-- General Parameters --> | 401 <!-- General Parameters --> |
777 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> | 814 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> |
778 <param name="myrimatch_max_peak" type="integer" value="100" | 815 <param name="myrimatch_max_peak" type="integer" value="100" |
779 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> | 816 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> |
780 </when> | 817 </when> |
781 </conditional> | 818 </conditional> |
819 | |
820 <!-- Andromeda ADVANCED PARAMETERS --> | |
821 <!-- Windows only | |
822 <conditional name="andromeda"> | |
823 <param name="andromeda_advanced" type="select" label="Andromeda Options"> | |
824 <option value="yes">Advanced</option> | |
825 <option value="no" selected="True">Default</option> | |
826 </param> | |
827 <when value="no" /> | |
828 <when value="yes"> | |
829 <param name="andromeda_max_pep_mass" type="float" value="4600.0" label="Andromeda maximum peptide mass, default is: 4600.0" /> | |
830 <param name="andromeda_max_comb" type="integer" value="250" label="Andromeda maximum combinations, default is: 250" /> | |
831 <param name="andromeda_top_peaks" type="integer" value="8" label="Andromeda number of top peaks, default is: 8" /> | |
832 <param name="andromeda_top_peaks_window" type="integer" value="100" label="Andromeda top peaks window width, default is: 100" /> | |
833 <param name="andromeda_incl_water" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for water losses, default is: true" /> | |
834 <param name="andromeda_incl_ammonia" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda account for ammonina losses, default is: true" /> | |
835 <param name="andromeda_neutral_losses" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda neutral losses are sequence dependent, default is: true" /> | |
836 <param name="andromeda_fragment_all" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Andromeda fragment all option, default is: false" /> | |
837 <param name="andromeda_emp_correction" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda emperical correction, default is: true" /> | |
838 <param name="andromeda_higher_charge" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Andromeda higher charge option, default is: true" /> | |
839 <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" /> | |
840 <param name="andromeda_frag_method" type="select" value="" label="Andromeda fragmentation method, (HCD, CID or EDT), default is: CID." > | |
841 <option value="CID" selected="true">CID</option> | |
842 <option value="HCD">HCD</option> | |
843 <option value="EDT">EDT</option> | |
844 </param> | |
845 <param name="andromeda_max_mods" type="integer" value="5" label="Andromeda maximum number of modifications, default is: 5" /> | |
846 <param name="andromeda_min_pep_length" type="integer" value="8" label="Andromeda minimum peptide length when using no enzyme, default is: 8" /> | |
847 <param name="andromeda_max_pep_length" type="integer" value="25" label="Andromeda maximum peptide length when using no enzyme, default is: 25" /> | |
848 <param name="andromeda_max_psms" type="integer" value="10" label="Andromeda maximum number of spectrum matches spectrum, default is: 10" /> | |
849 </when> | |
850 </conditional> | |
851 --> | |
782 | 852 |
783 <!-- Comet ADVANCED PARAMETERS --> | 853 <!-- Comet ADVANCED PARAMETERS --> |
784 <conditional name="comet"> | 854 <conditional name="comet"> |
785 <param name="comet_advanced" type="select" label="Comet Options"> | 855 <param name="comet_advanced" type="select" label="Comet Options"> |
786 <option value="yes">Advanced</option> | 856 <option value="yes">Advanced</option> |