--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_alignsets.xml	Wed May 30 15:34:37 2018 -0400
@@ -0,0 +1,53 @@
+<tool id="presto_alignsets" name="pRESTO AlignSets" version="@PRESTO_VERSION@">
+    <description>Multiple-align sequences with the same barcodes.</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    
+    <version_command>AlignSets.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$fastq_in' in.fastq &&
+        AlignSets.py muscle
+          --nproc "\${GALAXY_SLOTS:-1}"
+          -s in.fastq
+          --bf '$bf'
+          $div
+          --outname=tmp
+          #if $capture_log
+            --log '$log_out'
+          #end if
+    ]]></command>
+
+    <inputs>
+        <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file" help="FASTQ file of sequences with barcodes/UMIs in an annotation."/>
+        <param argument="--bf" type="text" value="BARCODE" label="Barcode Field" help="Name of the annotation field which contains the barcode/UMI sequence."/>
+        <param argument="--div" type="boolean" value="false" truevalue="--div" falsevalue="" label="Calculate Nucleotide Diversity" help="Specify to calculate nucleotide diversity of each set."/>
+        <expand macro="presto-log-param"/>
+    </inputs>
+
+    <outputs>
+        <data name="fastq_out" format="fastq" from_work_dir="tmp_align-pass.fastq"/>
+        <expand macro="presto-log-output"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="fastq_in" value="presto_alignsets_test_in.fastq"/>
+            <output name="fastq_out" file="presto_alignsets_test_out.fastq" compare="sim_size" delta="15"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Multiple aligns sequences with the same barcode to correct for any misalignments due to either different primer usage or insertions/deletions in the sequences.
+
+Only supports the "muscle" sub-command of pRESTO's AlignSets.py.
+
+See the `pRESTO online help <@PRESTO_URL_BASE@/AlignSets.html>`_ for more information.
+
+@HELP_NOTE@
+    ]]></help>
+    <expand macro="citations" />
+</tool>