Mercurial > repos > galaxyp > peptideshaker

comparison searchgui.xml @ 22:e3be595c0bf5 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 5ca27ef280bee8b65fd3d0d2cd5ff280a2cebb3d
author iracooke
date Fri, 07 Aug 2015 06:55:04 -0400
parents dfaea053e32f
children 913dbf2b83e0
comparison
equal deleted inserted replaced
21:dfaea053e32f 22:e3be595c0bf5
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
24 cp -r "\${SEARCHGUI_JAR_PATH%/*}" bin;
25 tmp_searchgui_jar_path=`echo "\$cwd/bin/\${SEARCHGUI_JAR_PATH\#\#/*/}"`;
26
23 #for $mgf in $peak_lists: 27 #for $mgf in $peak_lists:
24 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf" 28 #set $input_name = $mgf.display_name.replace(".mgf", "") + ".mgf"
25 ln -s -f '${mgf}' '${input_name}'; 29 ln -s -f '${mgf}' '${input_name}';
26 #end for 30 #end for
27 ##ln -s "${input_database}" input_database.fasta; 31 ##ln -s "${input_database}" input_database.fasta;
30 ########################################### 34 ###########################################
31 #### Creating decoy database #### 35 #### Creating decoy database ####
32 ########################################### 36 ###########################################
33 #if $create_decoy: 37 #if $create_decoy:
34 echo "Creating decoy database."; 38 echo "Creating decoy database.";
35 java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy && 39 java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.FastaCLI -in input_database.fasta -decoy &&
36 rm input_database.fasta && 40 rm input_database.fasta &&
37 cp input_database_concatenated_target_decoy.fasta input_database.fasta && 41 cp input_database_concatenated_target_decoy.fasta input_database.fasta &&
38 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta; 42 ## ln -sf input_database_concatenated_target_decoy.fasta input_database.fasta;
39 #end if 43 #end if
40 44
41 ##################################################### 45 #####################################################
42 ## generate IdentificationParameters for SearchGUI ## 46 ## generate IdentificationParameters for SearchGUI ##
43 ##################################################### 47 #####################################################
44 48
45 (java -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.IdentificationParametersCLI 49 (java -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.IdentificationParametersCLI
46 -out SEARCHGUI_IdentificationParameters.parameters 50 -out SEARCHGUI_IdentificationParameters.parameters
47 51
48 @GENERAL_PARAMETERS@ 52 @GENERAL_PARAMETERS@
49 53
50 -db input_database.fasta 54 -db input_database.fasta
245 && 249 &&
246 250
247 ################ 251 ################
248 ## Search CLI ## 252 ## Search CLI ##
249 ################ 253 ################
250 (java -Djava.awt.headless=true -cp \$SEARCHGUI_JAR_PATH eu.isas.searchgui.cmd.SearchCLI 254 (java -Djava.awt.headless=true -cp \$tmp_searchgui_jar_path eu.isas.searchgui.cmd.SearchCLI
251 -temp_folder `pwd` 255 -temp_folder `pwd`
252 -spectrum_files \$cwd 256 -spectrum_files \$cwd
253 -output_folder \$cwd/output 257 -output_folder \$cwd/output
254 -id_params SEARCHGUI_IdentificationParameters.parameters 258 -id_params SEARCHGUI_IdentificationParameters.parameters
255 259