diff hyphy_fubar.xml @ 24:c5ef306c2041 draft

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

--- a/hyphy_fubar.xml	Fri Apr 09 21:48:06 2021 +0000
+++ b/hyphy_fubar.xml	Tue Apr 20 10:24:45 2021 +0000
@@ -3,20 +3,24 @@
     <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[
-        ln -s '$input_file' fubar_input.fa &&
-        ln -s '$input_nhx' fubar_input.nhx &&
+        @SYMLINK_FILES@
         hyphy fubar
-            --alignment ./fubar_input.fa
-            --tree ./fubar_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --code '$gencodeid'
             --method '$posteriorEstimationMethod.method'
             --grid '$grid_points'
             @posteriorEstimationMethod_cmd@
             --concentration_parameter '$concentration'
-            > '$fubar_log'
+            > '$fubar_log' ;
+        @CATCH_ERROR@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -28,11 +32,11 @@
     </inputs>
     <outputs>
         <data name="fubar_log" format="txt"/>
-        <data name="fubar_output" format="hyphy_results.json" from_work_dir="fubar_input.fa.FUBAR.json" />
+        <data name="fubar_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>
-            <param name="input_file" ftype="fasta" value="fubar-in1.fa"/>
+            <param name="input_file" ftype="fasta.gz" value="fubar-in1.fa.gz"/>
             <param name="input_nhx" ftype="nhx" value="fubar-in1.nhx"/>
             <param name="posterior" value="Variational-Bayes"/>
             <output name="fubar_output" file="fubar-out1.json" compare="sim_size"/>