diff hyphy_absrel.xml @ 26:5f2ca10db92a draft

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

--- a/hyphy_absrel.xml	Tue Apr 20 19:53:39 2021 +0000
+++ b/hyphy_absrel.xml	Tue Apr 27 18:07:06 2021 +0000
@@ -1,28 +1,21 @@
 <?xml version="1.0"?>
-<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy1" profile="19.09">
     <description>adaptive Branch Site Random Effects Likelihood</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">aBSREL</token>
-        <token name="@operation@">absrel</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
+        ln -s '$absrel_output' ${input_file}.aBSREL.json &&
         @HYPHYMPI@ absrel
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
+            @INPUT_TREE@
             --code '$gencodeid'
-            --branches '$branches'
+            @branch_options@
             --output '$absrel_output'
             --multiple-hits $multiple_hits
-            #if $log:
-                > '$absrel_log'
-            #end if
-            ;
-        @CATCH_ERROR@
+        @ERRORS@
         ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -36,9 +29,6 @@
         <expand macro="branches"/>
     </inputs>
     <outputs>
-        <data name="absrel_log" format="txt">
-            <filter>log</filter>
-        </data>
         <data name="absrel_output" format="hyphy_results.json" />
     </outputs>
     <tests>
@@ -46,14 +36,12 @@
             <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
             <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
             <param name="multiple_hits" value="None" />
-            <param name="log" value="false"/>
             <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
         </test>
         <test>
             <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
             <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
             <param name="multiple_hits" value="Double" />
-            <param name="log" value="false"/>
             <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
         </test>
     </tests>