Mercurial > repos > dfornika > mentalist

changeset 1:a0a6d3e7416d draft

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planemo upload
author dfornika
date Thu, 14 Sep 2017 17:16:16 -0400
parents 071665c7c344
children 0f74aa0cfb68
files tools/mentalist_build.xml
diffstat 1 files changed, 3 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- 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>