# HG changeset patch
# User matt-shirley
# Date 1364695391 14400
# Node ID b9e8df2534f96c83589e4117b56fb781a676c38b

Uploaded

diff -r 000000000000 -r b9e8df2534f9 fixFastq.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fixFastq.xml	Sat Mar 30 22:03:11 2013 -0400
@@ -0,0 +1,26 @@
+<tool id="fixFastq" name="Fix barcodes" version="1.0.0">
+  <description> generated using Hamming encoding</description>
+  <command interpreter="python">fixFastq.py $strict $list $fastq $out</command>
+  <inputs>
+    <param format="text" name="strict" type="select" value=""/>
+      <label>Replace unknown barcodes with N</label>
+      <option value="">No</option>
+      <option value="-s">Yes</option>
+    <param format="tabular" name="list" type="data" label="List of barcodes used"/>
+    <param format="fastqsanger" name="fastq" type="data" label="Barcoded reads"/>
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="out"/>
+  </outputs>
+  <stdio>
+    <exit_code range="127" level="fatal" description="Cannot find fixFastq.py"/>
+  </stdio>
+  <requirements>
+    <requirement type="python-module">hamstring</requirement>
+  </requirements>
+  <help>
+    This program accepts a fastqsanger file containing reads that are barcoded on the 5' end using a Hamming7,4 DNA barcode. A list of valid barcodes is checked, 
+    and if the barcode checksum fails the barcode is corrected and checked against this list. If the barcode is not present in the list, it may be replaced 
+    with 'N' to denote ambiguity.
+  </help>
+</tool>