# HG changeset patch
# User dfornika
# Date 1505423776 14400
# Node ID a0a6d3e7416d30d5cac2d07003893938117d1609
# Parent  071665c7c3441fd31bbf8059c98188a9b30b2dd3
planemo upload

diff -r 071665c7c344 -r a0a6d3e7416d tools/mentalist_build.xml
--- a/tools/mentalist_build.xml	Tue Sep 05 18:52:15 2017 -0400
+++ b/tools/mentalist_build.xml	Thu Sep 14 17:16:16 2017 -0400
@@ -1,11 +1,10 @@
 <?xml version="1.0"?>
-<tool id="mentalist_build" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.2">
+<tool id="mentalist_build" name="MentaLiST Build DB" version="0.1.2">
   <requirements>
     <requirement type="package" version="0.1.2">mentalist</requirement>
   </requirements>
   <command detect_errors="exit_code">
   <![CDATA[
-	   mkdir mentalist-database && cd mentalist-database &&
 	   MentaLiST.jl
 	   build_db
 	   --db '$kmer_database'
@@ -13,9 +12,7 @@
 	   #if $profile
 	   -p '$profile'
 	   #end if
-	   -f ${" ".join(map(str, $input_fastas))} &&
-	   cd .. &&
-	   python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
+	   -f ${" ".join(map(str, $input_fastas))}
   ]]>
   </command>
   <inputs>
@@ -28,7 +25,7 @@
 	   label="Profile" help="Profile for known genotypes" />
   </inputs>
   <outputs>
-    <data name="out_file" format="data_manager_json" />
+    <data name="kmer_database" format="h5" />
   </outputs>
   <citations>
     <citation type="doi">10.1101/172858</citation>