Mercurial > repos > iuc > hyphy_slac

diff hyphy_slac.xml @ 24:ec499ddce7a9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author: iuc
date: Tue, 20 Apr 2021 10:28:55 +0000
parents: dc9e52b2d0e1
children: 0c6724c345d9
--- a/hyphy_slac.xml	Fri Apr 09 21:50:31 2021 +0000
+++ b/hyphy_slac.xml	Tue Apr 20 10:28:55 2021 +0000
@@ -3,20 +3,24 @@
     <description>Single Likelihood Ancestor Counting</description>
     <macros>
         <import>macros.xml</import>
+        <token name="@OPERATION@">SLAC</token>
+        <token name="@operation@">slac</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_file' slac_input.fa &&
-        ln -s '$input_nhx' slac_input.nhx &&
+        @SYMLINK_FILES@
         hyphy slac
-            --alignment ./slac_input.fa
-            --tree ./slac_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --code '$gencodeid'
             --branches '$branches'
             --samples '$number_of_samples'
             --pvalue '$p_value'
             --output '$slac_output'
-        > '$slac_log'
+        > '$slac_log' ;
+        @CATCH_ERROR@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>