Mercurial > repos > iuc > hyphy_absrel

diff hyphy_absrel.xml @ 24:9275e81b5590 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author: iuc
date: Tue, 20 Apr 2021 10:30:06 +0000
parents: 0b58ef9e84b2
children: 5f2ca10db92a
--- a/hyphy_absrel.xml	Fri Apr 09 21:51:00 2021 +0000
+++ b/hyphy_absrel.xml	Tue Apr 20 10:30:06 2021 +0000
@@ -3,14 +3,17 @@
     <description>adaptive Branch Site Random Effects Likelihood</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@OPERATION@">aBSREL</token>
+        <token name="@operation@">absrel</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_file' absrel_input.fa &&
-        ln -s '$input_nhx' absrel_input.nhx &&
+        @SYMLINK_FILES@
         @HYPHYMPI@ absrel
-            --alignment ./absrel_input.fa
-            --tree ./absrel_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --code '$gencodeid'
             --branches '$branches'
             --output '$absrel_output'
@@ -19,7 +22,7 @@
                 > '$absrel_log'
             #end if
             ;
-        @CATCH_MPIERR@
+        @CATCH_ERROR@
         ]]></command>
     <inputs>
         <expand macro="inputs"/>