diff hyphy_fubar.xml @ 26:cd41e7a4d35f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

--- a/hyphy_fubar.xml	Tue Apr 20 19:48:40 2021 +0000
+++ b/hyphy_fubar.xml	Tue Apr 27 18:04:56 2021 +0000
@@ -1,26 +1,22 @@
 <?xml version="1.0"?>
-<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_fubar" name="HyPhy-FUBAR" version="@VERSION@+galaxy1" profile="19.09">
     <description>Fast Unconstrained Bayesian AppRoximation</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">FUBAR</token>
-        <token name="@operation@">fubar</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
+        ln -s '$fubar_output' ${input_file}.FUBAR.json &&
         hyphy fubar
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
+            @INPUT_TREE@
             --code '$gencodeid'
             --method '$posteriorEstimationMethod.method'
             --grid '$grid_points'
             @posteriorEstimationMethod_cmd@
             --concentration_parameter '$concentration'
-            > '$fubar_log' ;
-        @CATCH_ERROR@
+        @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -31,7 +27,6 @@
 
     </inputs>
     <outputs>
-        <data name="fubar_log" format="txt"/>
         <data name="fubar_output" format="hyphy_results.json" />
     </outputs>
     <tests>