# HG changeset patch
# User iuc
# Date 1482360594 18000
# Node ID 404fae08ea3126b69e19015f914d023d2ccb09cf
# Parent  f7094efef9032c6e6344665f8917118e9240d61d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/bwameth commit f96ef202e742cc1d260bce023ae0d1e1499a11d8

diff -r f7094efef903 -r 404fae08ea31 bwameth.xml
--- a/bwameth.xml	Wed Sep 14 16:55:47 2016 -0400
+++ b/bwameth.xml	Wed Dec 21 17:49:54 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="bwameth" name="bwameth" version="0.2.0">
+<tool id="bwameth" name="bwameth" version="0.2.0.2">
     <description>Fast and accurate aligner of BS-Seq reads.</description>
     <requirements>
         <requirement type="package" version="1.2">samtools</requirement>
@@ -41,7 +41,7 @@
                 <option value="indexed">Use a built-in index</option>
             </param>
             <when value="history">
-                <param name="reference" type="data" format="fasta" metadata_name="dbkey" label="Select a genome" help="in FASTA format" />
+                <param name="reference" type="data" format="fasta" label="Select a genome" help="in FASTA format" />
             </when>
             <when value="indexed">
                 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
diff -r f7094efef903 -r 404fae08ea31 tool-data/bwameth_indexes.loc.sample
--- a/tool-data/bwameth_indexes.loc.sample	Wed Sep 14 16:55:47 2016 -0400
+++ b/tool-data/bwameth_indexes.loc.sample	Wed Dec 21 17:49:54 2016 -0500
@@ -1,10 +1,15 @@
 # This is a sample file distributed with Galaxy that is used to define a
 # list of bwa-meth indices, using three columns tab separated:
 #
-# bwameth_index_id\tSome description text\t/path/to/genome.fasta
+# <unique_build_id>	<dbkey>	<display_name>	<genome_fasta_file_path>
 #
 # An index can be created with the following command:
 #
 # bwameth.py index /some/path/genome.fa
 #
 # "/some/path/genome.fa" would then be the last column in the line
+# If this were for the mm10 mouse genome, the resulting entry would look like:
+#
+#mm9	mm9	Mouse (mm9)	/some/path/genome.fa
+#
+#
diff -r f7094efef903 -r 404fae08ea31 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Wed Sep 14 16:55:47 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Wed Dec 21 17:49:54 2016 -0500
@@ -1,6 +1,6 @@
 <tables>
-    <table name="bwameth_indexes" comment_char="#">
-        <columns>value, name, path</columns>
+    <table name="bwameth_indexes" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
         <file path="tool-data/bwameth_indexes.loc" />
     </table>
 </tables>