--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/jbrowse-fromdir.xml	Tue Dec 29 15:31:54 2015 -0500
@@ -0,0 +1,40 @@
+<tool id="jbrowse-upgrade" name="JBrowse - Data Directory to Standalone" version="0.3">
+  <description>upgrades the bare data directory to a full JBrowse instance</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command>python jbrowse.py --version</version_command>
+  <command><![CDATA[
+## Create output directory
+mkdir -p $output.files_path &&
+## Copy in jbrowse
+cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
+
+## Copy in data directory
+cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
+cat $output.files_path/index.html > $output
+]]></command>
+  <inputs>
+    <param label="JBrowse Data Directory"
+           name="input"
+           type="data"
+           help="Look for datasets with 'JBrowse ... Data Directory' in the name"
+           format="html" />
+  </inputs>
+  <outputs>
+      <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/>
+  </outputs>
+  <help><![CDATA[
+Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.
+
+@ATTRIBUTION@
+]]></help>
+  <tests>
+  </tests>
+  <citations>
+    <citation type="doi">10.1101/gr.094607.109</citation>
+  </citations>
+</tool>
+