Graham, How are the output files being handled in split_var_length_barcodes_wrapper.py? See http://wiki.g2.bx.psu.edu/Admin/Tools/Multiple%20Output%20Files for a reference-- you're going to want to follow the bottom example there involving $__new_file_path__ and the naming convention specified.
On a side note, this is something I've brushed up against recently myself, I'd be very interested in seeing what you come up with. -Dannon On Dec 5, 2011, at 6:47 AM, 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 > > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
