The option in the GUI for selecting multiple datasets for a single data parameter - causes multiple jobs to be created as you noted. If you just place multiple="true" on your data input parameter - that button will go away and all the datasets will be used for a single job.
If your tool consumes pairs of datasets - you will want to expose an option where you are using a parameter like:
<input name="input_pairs" type="data_collection" collection_type="list:paired" format="fastq" />
and then your users will have to use the data collection creator to pair off the datasets into a big list before using your tool - but the creator is actually really nice - I think it makes it very easy to build large lists of pairs.
Hope this helps - happy to provide more details, -John
On Fri, Jun 19, 2015 at 11:24 AM, Ryan G ngsbioinformatics@gmail.com wrote:
Hi all - I have a tool which is essentially an entire NGS pipeline bundled into a perl script and associated modules. I'd like to offer this tool to users via Galaxy.
I'm trying to pass a bunch of fastq files to the tool, but noticed that operating on multiple datasets creates a separate job for each dataset. I want to pass all the datasets to the tool so only one galaxy job is actually created. Is this possible, and if so, how do I go about doing this?
Ryan
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