--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/shhh.seqs.xml	Fri May 19 05:07:22 2017 -0400
@@ -0,0 +1,66 @@
+<tool profile="16.07" id="mothur_shhh_seqs" name="Shhh.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Denoise program (Quince SeqNoise)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$name" name.dat &&
+        ln -s "$group" group.dat &&
+
+        echo 'shhh.seqs(
+            fasta=fasta.dat,
+            name=name.dat,
+            #if $group:
+                group=group.dat,
+            #end if
+            sigma=$sigma,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/>
+        <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
+        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/>
+        <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="shhh_fasta" format_source="fasta" from_work_dir="fasta*.shhh_seqs.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
+        <data name="shhh_names" format="mothur.names" from_work_dir="fasta*.shhh_seqs.names" label="${tool.name} on ${on_string}: shhh.names"/>
+        <data name="shhh_map" format="txt" from_work_dir="fasta*.shhh_seqs.map" label="${tool.name} on ${on_string}: shhh.map"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
+            <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head.names"/>
+            <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/>
+            <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/>
+            <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The shhh.seqs_ command is a mothur-based rewrite of Chris Quince's sequence denoting program, SeqNoise.  Schloss prefers pre.cluster for this operation.
+
+.. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>