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[YABI-66] Take parameter value from defaults or custom #488

Closed ccgbuildbot closed 8 years ago

ccgbuildbot commented 8 years ago

[reporter="-1", created="Tue, 19 Mar 2013 12:52:10 +0800", resolved="Wed, 29 Oct 2014 11:44:42 +0800"]

Reported by s.williams@qfab.org, Aug 18, 2011
E.g. An aligner (bowtie) has a list of common genome references that most users could chose from, but some users will want to use their own reference sequence.

Currently the only way to support this seems to be by duplicating the tool.

Ideally, a user should be able to select from a dropdown of configured paths, or, in some way be able to indicate 'other' and select a loaded file or enter a path. The value from either method should go into option '-ref'.

ccgbuildbot commented 8 years ago

[author="tszabo", created="Wed, 29 Oct 2014 11:44:37 +0800"]

Something like this can (and should?) be implemented with a wrapper.
Just have a simple wrapper script that accepts -common-ref and -own-ref. The wrapper then calls the target application with using either -own-ref or -common-ref as -ref.