Mercurial > repos > galaxyp > peptideshaker

diff fasta_cli.xml @ 59:943a34df6047 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
author galaxyp
date Fri, 21 May 2021 19:13:14 +0000
parents 07ff622ec007
children 3ec27b4cee7c
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line diff
--- a/fasta_cli.xml	Sat Apr 10 15:57:17 2021 +0000
+++ b/fasta_cli.xml	Fri May 21 19:13:14 2021 +0000
@@ -28,7 +28,15 @@
         ###########################################
 
         echo 'Creating decoy database.' &&
-        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag &&
+        searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
+            --exec_dir="./bin/"
+            -use_log_folder 0
+            -temp_folder `pwd`
+            -in '${input_database.display_name}'
+            -decoy
+            -decoy_flag $database_processing_options.decoy_tag
+            -suffix $database_processing_options.decoy_type
+            -decoy_suffix $database_processing_options.decoy_file_tag &&
         mv '${output_db_name}' output
 ]]>
     </command>