Mercurial > repos > iuc > hyphy_prime

diff hyphy_prime.xml @ 15:296f6bc03fa6 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author: iuc
date: Tue, 20 Apr 2021 10:30:38 +0000
parents: 1d9d3c6bc246
children: 6d29207a32c5
--- a/hyphy_prime.xml	Fri Apr 09 21:51:27 2021 +0000
+++ b/hyphy_prime.xml	Tue Apr 20 10:30:38 2021 +0000
@@ -3,14 +3,17 @@
     <description>Property Informed Models of Evolution</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@OPERATION@">PRIME</token>
+        <token name="@operation@">prime</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_file' prime_input.fa &&
-        ln -s '$input_nhx' prime_input.nhx &&
+        @SYMLINK_FILES@
         @HYPHYMPI@ prime
-            --alignment ./prime_input.fa
-            --tree ./prime_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --code '$gencodeid'
             --branches '$branches'
             --pvalue '$p_value'
@@ -18,7 +21,7 @@
             --output '$prime_output'
             > '$prime_log'
             ;
-        @CATCH_MPIERR@
+        @CATCH_ERROR@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>