--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter-below-abund.xml	Sat Oct 17 04:02:33 2015 -0400
@@ -0,0 +1,50 @@
+<tool id="gedlab-khmer-filter-below-abund" name="Filter below abundance cutoff of 50" version="@WRAPPER_VERSION@-3">
+    <description>
+        Trims fastq/fasta sequences at k-mers with abundance below 50
+        based on a provided k-mer countgraph
+    </description>
+    <macros>
+        <token name="@BINARY@">filter-below-abund.py</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <expand macro="version" />
+    <command><![CDATA[
+set -xu &&
+#for $num, $input in enumerate($inputs)
+ln -s ${input} sequence-${num} &&
+mkdir output && cd output &&
+@BINARY@
+${input_countgraph_filename}
+../sequence*
+]]>
+    </command>
+    <inputs>
+        <expand macro="input_sequences_filenames" />
+        <expand macro="input_countgraph_filename" />
+    </inputs>
+    <outputs>
+        <collection name="sequence_files" type="list">
+            <discover_datasets pattern="__name__" directory="output" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="test-abund-read-2.fa" />
+            <param name="input_countgraph_filename" value="test-abund-read-2.large.oxlicg" ftype="oxlicg" />
+            <output_collection name="sequence_files">
+                <element name="sequence-0.below" file="test-abund-read-2.fa.below" />
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+Trims sequences at the first kmer with abundance above 50.
+
+@HELP_FOOTER@
+]]></help>
+    <citations>
+        <expand macro="software-citation" />
+        <expand macro="counting-citation" />
+    </citations>
+</tool>