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comparison searchgui.xml @ 12:d298e0b6fd72 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 464dc333f2e8d359265e1574b01386c4e7e9d840
author iracooke
date Tue, 11 Aug 2015 15:55:30 -0400
parents 76d14dc397ed
children 3ccfbb673089
comparison
equal deleted inserted replaced
11:76d14dc397ed 12:d298e0b6fd72
18 #set $temp_stderr = "searchgui_stderr" 18 #set $temp_stderr = "searchgui_stderr"
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;
24
25 cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
26 tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
27
23 #for $mgf in $peak_lists: 28 #for $mgf in $peak_lists:
24 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" 29 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
25 ln -s -f '${mgf}' '${input_name}'; 30 ln -s -f '${mgf}' '${input_name}';
26 #end for 31 #end for
27 ##ln -s "${input_database}" input_database.fasta; 32 ##ln -s "${input_database}" input_database.fasta;
30 ########################################### 35 ###########################################
31 #### Creating decoy database #### 36 #### Creating decoy database ####
32 ########################################### 37 ###########################################
33 #if $create_decoy: 38 #if $create_decoy:
34 echo "Creating decoy database."; 39 echo "Creating decoy database.";
35 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && 40 java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
36 rm input_database.fasta && 41 rm input_database.fasta &&
37 cp input_database_concatenated_target_decoy.fasta input_database.fasta && 42 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
38 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; 43 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
39 #end if 44 #end if
40 45
41 ##################################################### 46 #####################################################
42 ## generate IdentificationParameters for SearchGUI ## 47 ## generate IdentificationParameters for SearchGUI ##
43 ##################################################### 48 #####################################################
44 49
45 (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI 50 (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI
46 -out SEARCHGUI_IdentificationParameters.parameters 51 -out SEARCHGUI_IdentificationParameters.parameters
47 52
48 @GENERAL_PARAMETERS@ 53 @GENERAL_PARAMETERS@
49 54
50 -db input_database.fasta 55 -db input_database.fasta
245 && 250 &&
246 251
247 ################ 252 ################
248 ## Search CLI ## 253 ## Search CLI ##
249 ################ 254 ################
250 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 255 (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI
251 -temp_folder `pwd` 256 -temp_folder `pwd`
252 -spectrum_files \$cwd 257 -spectrum_files \$cwd
253 -output_folder \$cwd/output 258 -output_folder \$cwd/output
254 -id_params SEARCHGUI_IdentificationParameters.parameters 259 -id_params SEARCHGUI_IdentificationParameters.parameters
255 260