2011/5/20 Louise-Amélie Schmitt <louise-amelie.schm...@embl.de>:
> Hello
>
> Is there a way to check the file type with a conditional tag set within a
> tool?
>
> For example, if the tool can accept several file types but I have to make
> cheetah shut off some stuff for a couple of them?
>

You can do conditional code in the cheetah template using $input.ext
or $input.extension which both give you the Galaxy file type of an
input file parameter called $input.

For example, look at tools/fastx_toolkit/fastx_clipper.xml which does:

#if $input.ext == "fastqsanger":
 -Q 33
#end if

Alternatively, if you want to do this in the script being called by Galaxy,
just pass $input.ext as part of the command line.

Peter

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