diff hyphy_busted.xml @ 24:e2f03a50aace draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"

--- a/hyphy_busted.xml	Fri Apr 09 21:51:55 2021 +0000
+++ b/hyphy_busted.xml	Tue Apr 20 10:31:15 2021 +0000
@@ -3,18 +3,22 @@
     <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@OPERATION@">BUSTED</token>
+        <token name="@operation@">busted</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_file' busted_input.fa &&
-        ln -s '$input_nhx' busted_input.nhx &&
+        @SYMLINK_FILES@
         hyphy busted
-            --alignment ./busted_input.fa
-            --tree ./busted_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --code $gencodeid
             --branches '$branches'
             --output '$busted_output'
-            > '$busted_log'
+            > '$busted_log' ;
+        @CATCH_ERROR@
         ]]></command>
     <inputs>
         <expand macro="inputs"/>