--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fermi2.xml	Thu Jan 05 08:35:31 2017 -0500
@@ -0,0 +1,65 @@
+<tool id="fermi2" name="fermi2" version="0.14.dev1">
+    <description>assembles Illumina reads into unitigs</description>
+    <requirements>
+        <requirement type="package" version="r193">fermi2</requirement>
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        fermi2.pl unitig
+        -s$genome_size
+        -t\${GALAXY_SLOTS:-4}
+        -l$readlength
+        -p prefix "cat
+        #for fastq in $input1:
+            '$fastq'
+        #end for
+        "
+        -T $T
+        $two_pass_error
+        $E
+        > prefix.mak &&
+        make -f prefix.mak
+    ]]></command>
+    <inputs>
+        <param type="data" multiple="true" name="input1" format="fastqsanger,fastqsanger.gz"/>
+        <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/>
+        <param argument="-s" name="genome_size" type="integer" value="180000" min="1" label="approximate genome size in kilobases" help="Enter approximate genome size in kilobases. For a human genome of 3.2 gigabases enter 3200000"/>
+        <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/>
+        <param argument="-2" name="two_pass_error" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
+        <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/>
+    </inputs>
+    <outputs>
+        <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test.fastq.gz,test.fastq.gz"/>
+            <param name="readlength" value="150"/>
+            <param name="genome_size" value="1"/>
+            <output name="unitigs" file="unitigs.gz" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+fermi2 can assemble reads into unitigs.
+Unitig output can be further analysed by alignment to a reference genome using bwa-mem,
+and based on the alignment variants can be called using the fermi-variants tool.
+
+::
+
+  Usage:   fermi2.pl unitig [options] <in.fq>
+
+  Options: -p STR    output prefix [fmdef]
+           -s STR    approximate genome size [100m]
+           -2        2-pass error correction
+           -l INT    primary read length [101]
+           -T INT    use INT-mer for post-trimming/filtering [61]
+           -k INT    min overlap length during unitig construction [based on -l]
+           -o INT    min overlap length during graph cleaning [based on -l]
+           -m INT    min overlap length for unambiguous merging [based on -l]
+           -t INT    number of threads [4]
+           -E        don't apply error correction
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btv440</citation>
+    </citations>
+</tool>