Mercurial > repos > iuc > hyphy_meme

diff hyphy_meme.xml @ 2:b15d64d85c03 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
author iuc
date Fri, 14 Feb 2020 16:46:45 -0500
parents d02c8e6f7f2a
children 33040ebb30c6
line wrap: on
line diff
--- a/hyphy_meme.xml	Thu Feb 13 15:03:27 2020 -0500
+++ b/hyphy_meme.xml	Fri Feb 14 16:46:45 2020 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy0">
+<tool id="hyphy_meme" name="HyPhy-MEME" version="@VERSION@+galaxy1">
     <description>Mixed Effects Model of Evolution</description>
     <macros>
         <import>macros.xml</import>
@@ -8,12 +8,13 @@
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$input_file' meme_input.fa &&
         ln -s '$input_nhx' meme_input.nhx &&
-        @HYPHY_INVOCATION@ meme
+        @HYPHYMPI@ meme
             --alignment ./meme_input.fa
             --tree ./meme_input.nhx
             --code '$gencodeid'
             --branches '$branches'
             --pvalue '$p_value'
+            --output '$meme_output'
             > '$meme_log'
     ]]></command>
     <inputs>
@@ -24,7 +25,7 @@
     </inputs>
     <outputs>
         <data name="meme_log" format="txt"/>
-        <data name="meme_output" format="hyphy_results.json" from_work_dir="meme_input.fa.MEME.json"/>
+        <data name="meme_output" format="hyphy_results.json" />
     </outputs>
     <tests>
         <test>