Parsing input format in galaxy tools
Hi all, I'm writing a tool in Galaxy and I need to parse the input file's format (bam, bed, etc) to pass it as a variable to the command. Something like: command.sh $input ${input.format} $output Is there a way to get it? Bests, Nikos
Hi Nikos, try $input.ext ... Cheers, Bjoern
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's format (bam, bed, etc) to pass it as a variable to the command.
Something like:
command.sh $input ${input.format} $output
Is there a way to get it?
Bests, Nikos ___________________________________________________________ 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/
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Worked. Thanks Björn! 2014-02-14 19:41 GMT+01:00 Björn Grüning <bjoern.gruening@gmail.com>:
Hi Nikos,
try $input.ext ...
Cheers, Bjoern
Hi all,
I'm writing a tool in Galaxy and I need to parse the input file's format (bam, bed, etc) to pass it as a variable to the command.
Something like:
command.sh $input ${input.format} $output
Is there a way to get it?
Bests, Nikos ___________________________________________________________ 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/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (2)
-
Björn Grüning -
Nikos Sidiropoulos