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comparison searchgui.xml @ 24:815f93bb3e1b draft

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author galaxyp
date Fri, 06 Nov 2015 15:33:34 -0500
parents 913dbf2b83e0
children 3ef5a7dd1a36
comparison
equal deleted inserted replaced
23:913dbf2b83e0 24:815f93bb3e1b
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>