Hi Graham,

I've created something similar myself. I've not put it on the toolshed yet, as I have to test it further, but it seems to work as expected. See code in attachment.


Best regards,

geert vandeweyer
University of Antwerp


On 12/05/2011 12:47 PM, graham etherington (TSL) wrote:
Hi,
I'm developing a barcode splitter, which will split barcodes of variable
length and then put them into the history for downstream analysis
(currently FASTX barcode splitter only splits barcodes of the same length
and the user has to download the data through an html link). The number of
output files can't be determined until the tool has executed as it will
depend on the number of barcodes presented.
Here is an abridged version of the tool xml file:

<tool id="split_var_barcodes" name="Split barcodes of variable length"
version="1.0.0" force_history_refresh="True">
        <command interpreter="python">split_var_length_barcodes_wrapper.py 
$input
$barcodes $output.extra_files_path  $output</command>
<inputs>          <param format="txt" name="barcodes" type="data" 
label="Barcodes
to use" />
                <param format="fasta,fastqsanger,fastqsolexa,fastqillumina" 
name="input"
type="data" label="Library to split" />
        </inputs>
        
        <outputs>
                <data format="html" name="output" />
        </outputs>
</tool>

When I run the tool, the $output file to which I write various tool
progress stuff is written and is displayed in the history. Also, the spit
barcode files are written to a sub-directory of the same name as the
output file.
In the Galaxy database, if the $output file is named dataset_11940.dat
then an example barcode file name and path is:
/home/galaxy/software/galaxy-central/database/files/011/dataset_11940_files
/AACAGAGT.fastq

Unfortunately, the split barcode files are not being displayed in the
history, so I was wondering if anyone could see any problems in what I'm
doing.

Many thanks,
Graham




Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601




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Attachment: fastx_barcode_splitter.tar.gz
Description: GNU Zip compressed data

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