# HG changeset patch
# User thanhlv
# Date 1549575821 18000
# Node ID a7ccd6b0788e487c0111413fe082841bc48f6b75
# Parent  fcb4d9f67e75ca0dfb8af528868603c67f413342
planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/socru commit 1024f378b83203ab9c365a7d386981ad257ce1d1-dirty

diff -r fcb4d9f67e75 -r a7ccd6b0788e socru.xml
--- a/socru.xml	Thu Feb 07 12:21:46 2019 -0500
+++ b/socru.xml	Thu Feb 07 16:43:41 2019 -0500
@@ -6,6 +6,10 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
+
+        #set $_input_file = "'{}'".format($assembly.element_identifier)
+        ln -s '${assembly}' ${_input_file} &&
+
         socru 
 
         --threads \${GALAXY_SLOTS:-4}
@@ -13,7 +17,7 @@
         --top_blast_hits top_blast_hits.tsv
         
         #if str($opt_args.max_bases_from_ends) != ""
-            --max_bases_from_ends $max_bases_from_ends
+            --max_bases_from_ends $$opt_args.max_bases_from_ends
         #end if
         
         --not_circular $opt_args.not_circular
@@ -23,7 +27,7 @@
         #if $opt_args.verbose
             $opt_args.verbose
         #end if
-        $species $assembly
+        $species ${_input_file}
         > $output
     ]]></command>