diff hyphy_busted.xml @ 26:70fab57f3c05 draft

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

--- a/hyphy_busted.xml	Tue Apr 20 19:54:45 2021 +0000
+++ b/hyphy_busted.xml	Tue Apr 27 18:06:02 2021 +0000
@@ -1,33 +1,30 @@
 <?xml version="1.0"?>
-<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy1" profile="19.09">
     <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">BUSTED</token>
-        <token name="@operation@">busted</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
         hyphy busted
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
+            @INPUT_TREE@
             --code $gencodeid
-            --branches '$branches'
+            @branch_options@
             --output '$busted_output'
-            > '$busted_log' ;
-        @CATCH_ERROR@
+            @advanced_options@
+        @ERRORS@
         ]]></command>
     <inputs>
         <expand macro="inputs"/>
         <expand macro="gencode"/>
         <expand macro="branches"/>
+        <expand macro="srv"/>
     </inputs>
     <outputs>
-        <data name="busted_log" format="txt"/>
         <data name="busted_output" format="hyphy_results.json" />
+        <expand macro="alternative_model_output" />
     </outputs>
     <tests>
         <test>
@@ -35,6 +32,15 @@
             <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
             <output name="busted_output" file="busted-out1.json" compare="sim_size"/>
         </test>
+        <test>
+            <param name="input_file" ftype="nex" value="busted-in2.nex"/>
+            <param name="branches" value="specify" />
+            <param name="branch_label" value="B_US_90_WEAU160" />
+            <param name="srv_options" value="specify" />
+            <param name="save_alternative_model" value="true" />
+            <output name="busted_output" file="busted-out2-1.json" compare="sim_size"/>
+            <output name="alternative_model" file="busted-out2-2.json" compare="sim_size"/>
+        </test>
     </tests>
     <help><![CDATA[