--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse.xml	Mon May 04 17:21:38 2015 -0400
@@ -0,0 +1,44 @@
+<tool id="jbrowse" name="JBrowse" version="0.1">
+  <description>genome browser</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>python jbrowse.py --version</version_command>
+  <command interpreter="python"><![CDATA[jbrowse.py
+$positional_1
+
+#set data_files = '" "'.join([ str($var.gff3) for $var in $data_tracks ])
+#set data_formats  = '" "'.join([ str($var.gff3.ext) for $var in $data_tracks ])
+#set data_labels = '" "'.join([ str($var.gff3_label) for $var in $data_tracks ])
+
+--gff3 "$data_files"
+--gff3_format "$data_formats"
+--gff3_label "$data_labels"
+
+
+--jbrowse \${JBROWSE_SOURCE_DIR}
+--outdir $default.files_path
+> $default]]></command>
+  <inputs>
+    <param label="Genome" name="positional_1" type="data" format="fasta"/>
+    <repeat name="data_tracks" title="Annotation Track">
+        <param label="Annotation Data" help="in GFF, GFF3, or BED formats"
+            format="gff,gff3,bed" name="gff3" type="data"/>
+      <param label="Dataset Label" name="gff3_label" type="text"/>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="html" name="default" label="JBrowse on $positional_1.name"/>
+  </outputs>
+  <help><![CDATA[
+Deploy a static JBrowse visualization of a genome and some associated datasets
+
+@ATTRIBUTION@
+]]></help>
+  <citations>
+    <citation type="doi">10.1101/gr.094607.109</citation>
+  </citations>
+</tool>
+