--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter-abund.xml	Sat Oct 17 04:02:33 2015 -0400
@@ -0,0 +1,81 @@
+<tool id="gedlab-khmer-filter-abund" name="Filter by abundance" version="@WRAPPER_VERSION@-5">
+    <description>
+        Trims fastq/fasta sequences at k-mers of a given abundance
+        based on a provided k-mer countgraph
+    </description>
+    <macros>
+        <token name="@BINARY@">filter-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 ${input} filter-abund-sequence-${num} &&
+#end for
+mkdir output && cd output &&
+@BINARY@
+--cutoff=${cutoff}
+${variable_coverage}
+@THREADS@
+${input_countgraph_filename}
+../filter-abund-sequence*
+]]>
+    </command>
+    <inputs>
+        <expand macro="input_sequences_filenames" />
+        <param name="variable_coverage" type="boolean" checked="false" truevalue="--variable-coverage" falsevalue=""
+            label="Variable coverage"
+            help="Only trim when a sequence has high enough coverage; median abundance > 20 (--variable_coverage)" />
+        <param name="cutoff" type="integer" value="2" label="Cutoff"
+            help="Trim at k-mers below this abundance. (--cutoff)" />
+        <expand macro="input_countgraph_filename" />
+    </inputs>
+    <outputs>
+        <collection name="filter-abund-sequences" 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.oxlicg" ftype="oxlicg" />
+            <output_collection name="filter-abund-sequences" type="list">
+                <element name="filter-abund-sequence-0.abundfilt"> 
+                    <assert_contents>
+                        <has_text text="GGTTGACGGGGCTCAGGG" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+        <test>
+            <param name="inputs" value="test-abund-read-2.fa" />
+            <param name="input_countgraph_filename"
+                value="test-abund-read-2.oxlicg" ftype="oxlicg" />
+            <param name="cutoff" value="1" />
+            <output_collection name="filter-abund-sequences" type="list">
+                <element name="filter-abund-sequence-0.abundfilt">
+                    <assert_contents>
+                        <has_text text="GGTTGACGGGGCTCAGGG" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+Trim sequences at a minimum k-mer abundance.
+
+If the input sequences are from RNAseq or metagenome sequencing then
+`--variable-coverage` should be used.
+
+@HELP_FOOTER@
+]]>
+    </help>
+    <citations>
+        <expand macro="software-citation" />
+        <expand macro="counting-citation" />
+    </citations>
+</tool>