# HG changeset patch
# User jjohnson
# Date 1651005335 0
# Node ID 73fd7703a7433365b7c776505bab4ce863ee1b70
# Parent  8ed8af5836d1c91ce35ece699e6834f4416cde4e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit fe2e3c7429c5bea23690a27b5889b502984ad58a"

diff -r 8ed8af5836d1 -r 73fd7703a743 arriba.xml
--- a/arriba.xml	Tue Apr 26 20:21:29 2022 +0000
+++ b/arriba.xml	Tue Apr 26 20:35:35 2022 +0000
@@ -13,6 +13,30 @@
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
 @GENOME_SOURCE@
+#if $blacklist
+    #if $blacklist.is_of_type('tabular.gz')
+        #set $blacklist_file = 'blacklist.tsv.gz'
+        ln -sf '$blacklist'  $blacklist_file &&
+    #else
+        #set $blacklist_file = $blacklist
+    #end if
+#end if
+#if $known_fusions
+    #if $known_fusions.is_of_type('tabular.gz')
+        #set $known_fusions_file = 'known_fusions.tsv.gz'
+        ln -sf '$known_fusions'  $known_fusions_file &&
+    #else
+        #set $known_fusions_file = $known_fusions
+    #end if
+#end if
+#if $tags
+    #if $tags.is_of_type('tabular.gz')
+        #set $tags_file = 'tags.tsv.gz'
+        ln -sf '$tags'  $tags_file &&
+    #else
+        #set $tags_file = $tags
+    #end if
+#end if
 #if str($input_params.input_source) == "use_fastq"
     #set $readFilesCommand = ''
     #set $read2 = ''
@@ -45,30 +69,6 @@
     #else 
         #set $star_index_dir = $input_params.index.arriba_ref.fields.star_index
     #end if
-    #if $blacklist
-        #if $blacklist.is_of_type('tabular.gz')
-            #set $blacklist_file = 'blacklist.tsv.gz'
-            ln -sf '$blacklist'  $blacklist_file &&
-        #else
-            #set $blacklist_file = $blacklist
-        #end if
-    #end if
-    #if $known_fusions
-        #if $known_fusions.is_of_type('tabular.gz')
-            #set $known_fusions_file = 'known_fusions.tsv.gz'
-            ln -sf '$known_fusions'  $known_fusions_file &&
-        #else
-            #set $known_fusions_file = $known_fusions
-        #end if
-    #end if
-    #if $tags
-        #if $tags.is_of_type('tabular.gz')
-            #set $tags_file = 'tags.tsv.gz'
-            ln -sf '$tags'  $tags_file &&
-        #else
-            #set $tags_file = $tags
-        #end if
-    #end if
 
     STAR 
     --runThreadN \${GALAXY_SLOTS:-1}