Question: my tool and collections
gravatar for michael.palumbo
3 months ago by
michael.palumbo0 wrote:


I want to do something related to writing my own tool (in perl) and 'collections'. I haven't found any relevant docs. If I've missed them - my apologies - please post a link and i'll dig in.

Big picture, I want the user to select a (single) 'collection' as an argument to my tool (via the center panel in Galaxy) and I want to pass the individual elements that comprise the collection to my tool (which is written in perl). I'll assume that passing a 'collection' to the perl script isn't possible since perl has no idea what a collection is.

For example, let's assume the user has created a 'collection' that contains NGS data from an Illumina MiSeq sequencing run, let's say 7 samples were sequenced. The collection would contain 14 data objects, one forward and one reverse pair for each of the 7 samples. (I'm not thoroughly familiar with collections nomenclature, so maybe the proper way to describe this is that the collection is a list of 7 paired collections? anyway...)

After the user selects my tool in the left panel of the tools listing, they select the collection via the center panel in Galaxy and, somewhere transparent to the user (in the XML tool config?), the collection is unwound (my words) and the individual data items are passed to the perl script. the number of items passed to the perl script may vary from run to run, because the number of forward/reverse pairs, ie, samples processed, in a collection would likely vary from run to run.

is this possible?

Also... if there's some other way to allow the user to pick just one data object and have my tool operate on an entire set of paired-end NGS read files, i'm open to suggestions.


ADD COMMENTlink modified 3 months ago by Martin Čech ♦♦ 4.8k • written 3 months ago by michael.palumbo0
gravatar for Martin Čech
3 months ago by
Martin Čech ♦♦ 4.8k
United States
Martin Čech ♦♦ 4.8k wrote:

I think all of this is possible and the (paired) collection as input would be the best way.

Our documentation for tool writing is at including many examples with collections. If you have any concrete questions please raise them also. You can also reach our community of experienced tool developers at

ADD COMMENTlink written 3 months ago by Martin Čech ♦♦ 4.8k
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