--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tn93_cluster.xml	Fri Apr 23 03:04:15 2021 +0000
@@ -0,0 +1,71 @@
+<tool id="tn93_cluster" name="TN93 Cluster" version="@VERSION@">
+    <description>sequences that lie within a specific distance of each other</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">tn93</requirement>
+        <requirement type="package" version="3.9">python</requirement>
+    </requirements>
+    <version_command><![CDATA[tn93 --version]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    python '$__tool_directory__/tn93_cluster.py' --input '$input_fasta' --reference '$reference' --output '$tn93_clusters'
+        --threshold $threshold
+        --ambigs $ambigs
+        --cluster-type $cluster_type
+        --overlap $overlap
+        --fraction $fraction
+        --cluster-count $cluster_count
+        #if $compress:
+            --compressed '$tn93_compressed_clusters'
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="input_fasta" type="data" format="fasta" label="Input in FASTA format" />
+        <param name="reference" type="data" format="fasta" label="Reference in FASTA format" />
+        <param argument="--compress" type="boolean" truevalue="--compress" falsevalue="" label="Output additional fasta dataset with compressed clusters" />
+        <param argument="--cluster-count" type="integer" value="200" label="Only retain this many clusters" />
+        <param argument="--threshold" type="float" min="0" value="0.0005" label="Distance threshold" help="Sequences which lie within this distance will be clustered" />
+        <param argument="--ambigs" type="select" label="Strategy for ambiguous nucleotides">
+            <option value="resolve" selected="true">resolve</option>
+            <option value="average">average</option>
+            <option value="skip">skip</option>
+            <option value="gapmm">gapmm</option>
+        </param>
+        <param  argument="--cluster_type" type="select" label="Clustering rules" help="&quot;All&quot;: Each sequence within the cluster must be within the specified distance of every other sequence in the cluster. &quot;Any&quot;: Each sequence within the cluster must be within the specified distance of at least one other sequence.">
+            <option value="all">All</option>
+            <option value="any">Any</option>
+        </param>
+        <param name="overlap" argument="-l" type="integer" value="100"
+            label="Only process pairs that overlap by at least N bases" />
+        <param name="fraction" argument="-g" type="float" value="1.0"
+            label="Maximum tolerated fraction of ambiguous characters" />
+    </inputs>
+    <outputs>
+        <data format="json" name="tn93_clusters" />
+        <data format="fasta" name="tn93_compressed_clusters">
+            <filter>compress</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="input_fasta" value="cluster-in1-1.fa" />
+            <param name="reference" value="cluster-in1-2.fa" />
+            <param name="threshold" value="0.35" />
+            <param name="compress" value="true" />
+            <output file="cluster-out1.json" ftype="json" name="tn93_clusters" />
+            <output file="cluster-out1.fa" ftype="fasta" name="tn93_compressed_clusters" />
+        </test>
+    </tests>
+    <help><![CDATA[
+TN93-Cluster
+============
+
+Clusters sequences within a minimum distance of each other using the 1993
+Tamura-Nei distance calculation.
+
+]]></help>
+    <expand macro="citations">
+        <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
+    </expand>
+</tool>