Mercurial > repos > msjeon > abyss_tool

diff abyss_toolsuite-92636934a189/abyss/abyss.xml @ 0:ce99b6666d1f draft

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author msjeon
date Mon, 11 Jun 2012 14:48:15 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abyss_toolsuite-92636934a189/abyss/abyss.xml	Mon Jun 11 14:48:15 2012 -0400
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+<tool id="abyss" name="Abyss" version="1.0.0">
+<description>Assemble short unpaired reads</description>
+<command interpreter='bash'>abyss_wrapper.sh $k $infile $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>