diff tools/ilmn_pacbio/abyss.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ilmn_pacbio/abyss.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,30 @@
+<tool id="abyss" name="ABySS" version="1.0.0">
+  <description>Short-read de Bruijn assembly</description>
+  <command interpreter="python">
+    quake_wrapper.py -k $k -r $input1 -p 8 > $output1
+  </command>
+  <inputs>
+    <param name="input1" format="fastq" type="data" label="Select FASTQ file to correct" />
+    <param name="k" type="integer" value="16" label="Size of k-mers to correct" />
+  </inputs>
+  <outputs>
+    <data format="fastq" name="output1" label="Error-corrected reads from ${on_string}" />
+  </outputs>
+  <help>
+
+**What it does**
+
+TBD.  Calls ABySS assembler
+
+**Parameter list**
+
+k
+
+**Output**
+
+Corrected reads
+
+  </help>
+</tool>
+
+