--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dada2_derepFastq.xml	Fri Mar 08 06:33:55 2019 -0500
@@ -0,0 +1,37 @@
+<tool id="dada2_derepFastq" name="dada2: derepFastq" version="@DADA2_VERSION@">
+    <description>dereplicate amplicon sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+	mkdir '$derep.extra_files_path' &&
+    Rscript '$dada2_script'
+    ]]></command>
+    <configfiles>
+        <configfile name="dada2_script"><![CDATA[
+library(dada2, quietly=T)
+derep <- derepFastq('$reads')
+
+write.table(derep\$uniques, file = '$derep', quote = F, sep = "\t", row.names = T, col.names = F)
+saveRDS(derep, file=file.path('$derep.extra_files_path', "Rdata"))
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data" />
+    </inputs>
+    <outputs>
+        <data name="derep" format="dada2_derep" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="reads" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" />
+            <output name="output" value="derepFastq_single_F3D0_R1.table" ftype="dada2_derep" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>