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Question: How to pass the genome name or dbkey to a tool
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gravatar for Brad Langhorst
4.5 years ago by
Brad Langhorst • 100
United States
Brad Langhorst • 100 wrote:

I'd like to pass the name or dbkey of a reference genome (e.g. hg19) to a tool .

How can I set up a variable to pass to my tool without asking the user to specify the refernece again (i.e. infer the reference from the bam file) ?

E.g.
I have a BAM file in the tool xml 

<param name='bam_file'          type='data'     optional='false'  format='bam'      label="Aligned reads (bam)" />

I want to call the tool like this:

tool_name.py --reference_genome=$dbkey
tool • 1.3k views
ADD COMMENT • link •
modified 4.5 years ago • written 4.5 years ago by Brad Langhorst • 100
3
gravatar for Daniel Blankenberg
4.5 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:

You can do something like this:

tool_name.py --reference_genome="${ bam_file.dbkey }"
ADD COMMENT • link written 4.5 years ago by Daniel Blankenberg ♦♦ 1.7k

Excellent... where can I find more information about bam_file object's methods?

(I'd also like to get the genome size if I can.)

ADD REPLY • link written 4.5 years ago by Brad Langhorst • 100
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