--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/preprocessing.xml	Thu Feb 26 18:16:36 2015 -0500
@@ -0,0 +1,53 @@
+<tool id="PHYLO_preprocessing" name="Preprocess sequences" version="2.0.0">
+  <description>in preparation for phylogenetic placement</description>
+  <requirements>
+    <requirement type="package">yapp_env</requirement>
+  </requirements>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <version_command>echo "guppy $(guppy --version)"</version_command>
+  <command interpreter="bash">
+    preprocessing-wrapper.sh ${config}
+  </command>
+  <stdio>
+    <expand macro="basic_errors"/>
+  </stdio>
+  <inputs>
+    <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
+    <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
+    <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
+  </inputs>
+  <outputs>
+    <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/>
+    <data name="dedup_info" format="csv" label="Deduplication info"/>
+    <data name="aligned_seqs" format="fasta" label="Aligned sequences"/>
+    <data name="aligned_scores" format="txt" label="Alignment scores"/>
+  </outputs>
+  <configfiles>
+    <configfile name="config">
+REFPKG="${refpkg.extra_files_path}"
+INPUT_SEQS="${input_seqs}"
+SPLIT_MAP="${split_map}"
+
+DEDUP_SEQS="${dedup_seqs}"
+DEDUP_INFO="${dedup_info}"
+ALIGNED_SEQS="${aligned_seqs}"
+ALIGNED_SCORES="${aligned_scores}"
+    </configfile>
+  </configfiles>
+  <!-- The contents of the help tag is parsed as reStructuredText. Please see
+       help-template.rst for examples of commonly-used sections in other Galaxy
+       tools. -->
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool aligns query sequences with the reference sequences used to make the
+reference tree contained in the reference package and then merges the query and
+reference sequences.
+
+  </help>
+</tool>