Mercurial > repos > matt-shirley > hamstring
changeset 0:b9e8df2534f9 draft
Uploaded
| author | matt-shirley |
|---|---|
| date | Sat, 30 Mar 2013 22:03:11 -0400 |
| parents | |
| children | 7911d648cf29 |
| files | fixFastq.xml |
| diffstat | 1 files changed, 26 insertions(+), 0 deletions(-) [+] |
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--- /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>