--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/do-partition.xml	Sat Oct 17 04:02:33 2015 -0400
@@ -0,0 +1,58 @@
+<tool id="gedlab-khmer-do-partition" name="Sequence partition all-in-one" version="@WRAPPER_VERSION@-4">
+    <description>Load, partition, and annotate FAST[AQ] sequences</description>
+    <macros>
+        <token name="@BINARY@">do-partition.py</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version" />
+    <command><![CDATA[
+set -xu &&
+#for $num, $input in enumerate($inputs)
+ln -s ${input} sequence-${num} &&
+#end for
+mkdir -p output && cd output &&
+@BINARY@
+@TABLEPARAMS@
+@THREADS@
+output
+../sequence-*
+&&
+mv output.info $information
+]]>
+    </command>
+    <inputs>
+        <expand macro="input_sequences_filenames" />
+        <expand macro="tableinputs" />
+    </inputs>
+    <outputs>
+        <data name="information" format="txt" label="${tool.name} summary." />
+        <collection name="annotated_sequence_files" type="list">
+            <discover_datasets pattern="__name__" directory="output" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="random-20-a.fa"/>
+            <output_collection name="annotated_sequence_files" type="list">
+                <element name="sequence-0.part" file="random-20-a.fa.part" />
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+Load in a set of sequences, partition them, merge the partitions, and
+annotate the original sequences files with the partition information.
+
+This script combines the functionality of `load-graph.py`,
+`partition-graph.py`, `merge-partitions.py`, and
+`annotate-partitions.py` into one script. This is convenient
+but should probably not be used for large data sets, because
+`do-partition.py` doesn't provide save/resume functionality.
+]]>
+    </help>
+    <citations>
+        <expand macro="software-citation" />
+        <expand macro="graph-citation" />
+    </citations>
+</tool>