--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment.xml	Thu May 21 03:58:09 2015 -0400
@@ -0,0 +1,66 @@
+<tool id="vsearch_alignment" name="VSearch alignment" version="@VERSION@.0">
+    <description></description>
+    <macros>
+        <import>vsearch_macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version_command" />
+    <command>
+<![CDATA[
+    vsearch
+        @GENERAL@
+        $acceptall
+        --id $id
+        --iddef $iddef
+        --allpairs_global "$infile"
+        --alnout $outfile
+        --query_cov $query_cov
+        @USERFIELDS@
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Select your FASTA file" help="(--allpairs_global)" />
+        <expand macro="id_and_iddef" />
+        <param name="acceptall" type="boolean" truevalue="--acceptall" falsevalue="" checked="False" 
+            label="Output all pairwise alignments" help="This option overrides all other accept/reject options including identity. (--acceptall)"/>
+        <param name="query_cov" type="float" value="" optional="True" label="Reject if fraction of query seq. aligned lower than this value"
+            help="(--query_cov)"/>
+        <expand macro="userfields" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="Rfam_11_0.repr.fasta.bz2" ftype="fasta" />
+            <param name="acceptall" value=""/>
+            <param name="id" value="0.97"/>
+            <param name="query_cov" value="0.95"/>
+            <param name="userfields" value="query,target"/>
+            <output name="outfile" file="alignment_result1.fasta" lines_diff="4" ftype="fasta" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Pairwise alignments of all sequences.
+
+
+Alignment options (most searching options also apply)
+  --allpairs_global FILENAME  perform global alignment of all sequence pairs
+  --alnout FILENAME           filename for human-readable alignment output
+  --acceptall                 output all pairwise alignments
+
+@EXTERNAL_DOCUMENTATION@
+
+-------
+
+@REFERENCES@
+
+
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>