diff hyphy_meme.xml @ 23:2f07f5b4e47b draft

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

--- a/hyphy_meme.xml	Fri Apr 09 21:47:38 2021 +0000
+++ b/hyphy_meme.xml	Tue Apr 20 10:24:10 2021 +0000
@@ -1,29 +1,34 @@
 <?xml version="1.0"?>
-<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0" profile="19.09">
+<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1" 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[
-        ln -s '$input_file' meme_input.fa &&
-        ln -s '$input_nhx' meme_input.nhx &&
+        @SYMLINK_FILES@
         @HYPHYMPI@ meme
-            --alignment ./meme_input.fa
-            --tree ./meme_input.nhx
+            --alignment ./$input_file
+            #if $input_nhx:
+                --tree ./input.nhx
+            #end if
             --code '$gencodeid'
             --branches '$branches'
             --pvalue '$p_value'
             --output '$meme_output'
+            --full-model '$full_model'
             > '$meme_log'
             ;
-        @CATCH_MPIERR@
+        @CATCH_ERROR@
     ]]></command>
     <inputs>
         <expand macro="inputs"/>
         <expand macro="gencode"/>
         <expand macro="branches"/>
         <param name="p_value" type="float" value=".1" min="0" max="1" label="P-value threshold"/>
+        <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"/>