Mercurial > repos > iuc > colibread_takeabreak

diff takeabreak.xml @ 1:bcdeb3c92e9f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
author: iuc
date: Fri, 24 Nov 2017 12:47:05 -0500
parents: 6b5ba7c3fb7c
children: ac147b863f6b
--- a/takeabreak.xml	Fri Oct 20 03:13:08 2017 -0400
+++ b/takeabreak.xml	Fri Nov 24 12:47:05 2017 -0500
@@ -13,7 +13,7 @@
         #if str( $input_type_option.input_type ) == "simple"
             #for $input in $input_type_option.reads
                 #if $input
-                    #set $filename = str($input)+ "." + $input.ext
+                    #set $filename = os.path.basename(str($input)) + "." + $input.ext
                     ln -sf '${input}' '${filename}' &&
                     echo "${filename}" >> input.fof &&
                 #end if
@@ -22,7 +22,7 @@
             ## if paired reads in a list
             #for $i, $list in enumerate( $input_type_option.reads_lists )
                 #for $read in $list.list_reads
-                    #set $filename = str($read) + "." + $read.ext
+                    #set $filename = os.path.basename(str($read)) + "." + $read.ext
                     ln -sf '${read}' '${filename}' &&
                     echo "${filename}" >> "indiv_${i}.fof" &&
                 #end for