--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readreduce.xml	Wed Jul 17 13:41:47 2019 -0400
@@ -0,0 +1,69 @@
+<tool id="tn93_readreduce" name="Merge matching reads" version="@VERSION@">
+    <description>into clusters with TN-93</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">tn93</requirement>
+    </requirements>
+    <version_command><![CDATA[tn93 --version]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    readreduce
+    -q
+    -o '$output'
+    #if str($options.advanced) == 'advanced':
+        -a $options.ambigs
+        -l $options.overlap
+        #if $options.counts_in_name:
+            -d '$options.counts_in_name'
+        #end if
+        -s '$size'
+    #end if
+    '$input'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Input in FASTA format" />
+        <conditional name="options">
+            <param label="Additional options" name="advanced" type="select">
+                <option value="defaults">Use defaults</option>
+                <option value="advanced">Specify additional parameters</option>
+            </param>
+            <when value="defaults" />
+            <when value="advanced">
+                <param name="size" argument="-s" type="integer" min="0" value="18" label="Mimimum cluster size to report in output" />
+                <param name="ambigs" argument="-a" type="select" label="Strategy for ambiguous nucleotides">
+                    <option value="handle">handle</option>
+                    <option value="resolve">resolve</option>
+                    <option value="average">average</option>
+                    <option value="skip">skip</option>
+                    <option value="gapmm">gapmm</option>
+                </param>
+                <param name="overlap" argument="-l" type="integer" value="100"
+                    label="Only count pairs that overlap by at least N bases" />
+                <param name="counts_in_name" argument="-d" type="text"
+                    optional="true" label="Sequence name component immediately preceding a copy number" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="readreduce-in1.fa" />
+            <output file="readreduce-out1.fa" ftype="fasta" name="output" sort="True" />
+        </test>
+        <test>
+            <param name="input" value="readreduce-in2.fa" />
+            <output file="readreduce-out2.fa" ftype="fasta" name="output" sort="True" />
+        </test>
+    </tests>
+    <help><![CDATA[
+readreduce
+----------
+
+Merge matching reads into clusters using the
+[Tamura Nei 93 distance](http://www.ncbi.nlm.nih.gov/pubmed/8336541) algorithm.
+]]></help>
+    <expand macro="citations" />
+</tool>