diff abyss.xml @ 0:1d0f1274d999 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss.xml	Tue Apr 14 22:47:01 2015 -0400
@@ -0,0 +1,34 @@
+<tool id="abyss" name="Abyss" version="1.0.0">
+    <description>Assemble short unpaired reads</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+ABYSS -k$k $infile -o $outfile
+]]>
+    </command>
+
+    <inputs>
+        <param name="infile" type="data" format="fasta|fastq" label="Unpaired read sequences" />
+        <param name="k" type="integer" value="41" label="K-mer size" help="Try multiple sizes, starting around 2/3 read length" />
+    </inputs>
+
+    <outputs>
+        <data name="outfile" format="fasta" />
+    </outputs>
+
+    <help>
+**What it does**
+
+ABySS is a de novo sequence assembler that is designed for short reads.
+
+.. image:: http://www.bcgsc.ca/platform/bioinfo/software/abyss/screenshot
+
+**Reference**
+
+http://www.bcgsc.ca/platform/bioinfo/software/abyss
+    </help>
+</tool>