# HG changeset patch
# User iuc
# Date 1656005330 0
# Node ID d110a41418988fc39f56e0a736c575921dba51a5
# Parent  a04e64efa43a22e210218e7d75f079346a275256
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ragtag commit 6add25f561c83df53d3e1302a7067ff33409b071

diff -r a04e64efa43a -r d110a4141898 macros.xml
--- a/macros.xml	Wed Nov 10 23:33:13 2021 +0000
+++ b/macros.xml	Thu Jun 23 17:28:50 2022 +0000
@@ -67,8 +67,8 @@
         </conditional>
     </xml>
     <token name="@INPUTS@"><![CDATA[
-        $mode_conditional.reference
-        $mode_conditional.query
+        reference.fa
+        query.fa
     ]]></token>
     <token name="@COMMON_PARAMETERS@"><![CDATA[
         --aligner $mode_conditional.advanced_options.mapping_conditional.mapping_option 
diff -r a04e64efa43a -r d110a4141898 ragtag.xml
--- a/ragtag.xml	Wed Nov 10 23:33:13 2021 +0000
+++ b/ragtag.xml	Thu Jun 23 17:28:50 2022 +0000
@@ -23,6 +23,15 @@
         #end for
         #set $merge_files = " ".join($input_files)
     #end if
+
+    ## symlink reference because a .fai file is created
+    #if $mode_conditional.mode_option in ['correct', 'scaffold', 'patch']
+        ln -s '$mode_conditional.reference' reference.fa &&
+        ln -s '$mode_conditional.query' query.fa &&
+    #else
+        ln -s '$assembly_fasta' assembly.fa &&
+    #end if
+
     ragtag.py $mode_conditional.mode_option -u
     #if $mode_conditional.mode_option == 'correct'
         @INPUTS@
@@ -72,7 +81,7 @@
             $mode_conditional.advanced_options.patching_mode
         #end if
     #else
-        $assembly_fasta
+        assembly.fa
         #if $mode_conditional.scaffold_files
             $merge_files
         #end if