--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/bwa_index_builder.xml	Fri Mar 28 14:18:43 2014 -0400
@@ -0,0 +1,33 @@
+<tool id="bwa_index_builder_data_manager" name="BWA index" tool_type="manage_data" version="0.0.1">
+    <description>builder</description>
+    <requirements>
+        <requirement type="package" version="0.5.9">bwa</requirement>
+    </requirements>
+    <command interpreter="python">bwa_index_builder.py "${out_file}" --fasta_filename "${all_fasta_source.fields.path}" --fasta_dbkey "${all_fasta_source.fields.dbkey}" --fasta_description "${all_fasta_source.fields.name}" --data_table_name "bwa_indexes"</command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param type="text" name="sequence_name" value="" label="Name of sequence" />
+        <param type="text" name="sequence_id" value="" label="ID for sequence" />
+        
+        <param name="index_algorithm" type="select" label="Algorithm for constructing BWT index">
+            <option value="automatic" selected="True" help="1GB cut-off">Guess automatically</option>
+            <option value="is" hel="Small genomes">IS linear-time algorithm</option>
+            <!-- <option value="div">div</option> -->
+            <option value="bwtsw" help="Large genomes">BWT-SW</option>
+        </param>
+        
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json"/>
+    </outputs>
+
+    <help>
+
+.. class:: infomark
+
+**Notice:** If you leave name, description, or id blank, it will be generated automatically. 
+
+    </help>
+</tool>