diff hyphy_meme.xml @ 25:e0763df98352 draft

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

--- a/hyphy_meme.xml	Tue Apr 20 19:48:07 2021 +0000
+++ b/hyphy_meme.xml	Tue Apr 27 17:59:28 2021 +0000
@@ -1,27 +1,21 @@
 <?xml version="1.0"?>
-<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1" profile="19.09">
+<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy2" profile="19.09">
     <description>Mixed Effects Model of Evolution</description>
     <macros>
         <import>macros.xml</import>
-        <token name="@OPERATION@">MEME</token>
-        <token name="@operation@">meme</token>
     </macros>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
         @SYMLINK_FILES@
         @HYPHYMPI@ meme
             --alignment ./$input_file
-            #if $input_nhx:
-                --tree ./input.nhx
-            #end if
+            @INPUT_TREE@
             --code '$gencodeid'
-            --branches '$branches'
+            @branch_options@
             --pvalue '$p_value'
             --output '$meme_output'
             --full-model '$full_model'
-            > '$meme_log'
-            ;
-        @CATCH_ERROR@
+        @ERRORS@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
@@ -31,7 +25,6 @@
         <param argument="--full-model" type="boolean" truevalue="Yes" falsevalue="No" label="Perform branch length re-optimization under the full codon model" />
     </inputs>
     <outputs>
-        <data name="meme_log" format="txt"/>
         <data name="meme_output" format="hyphy_results.json" />
     </outputs>
     <tests>