Re: [galaxy-dev] Tools: dynamic check of file type?

[Louise-Amélie Schmitt]

Well I'm still missing something...

Is there a way to use the conditional tag sets in the tool's xml with 
it? To suppress the unnecessary options for a given file type? or more 
than one?


regards,
L-A


Le 20/05/2011 13:15, Louise-Amélie Schmitt a écrit :

It's exactly what I needed!!!

Thanks a lot!
L-A


Le 20/05/2011 12:29, Peter Cock a écrit :

2011/5/20 Louise-Amélie Schmittlouise-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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Re: [galaxy-dev] Tools: dynamic check of file type?

[Peter Cock]

2011/5/20 Louise-Amélie Schmitt louise-amelie.schm...@embl.de:
 Well I'm still missing something...

 Is there a way to use the conditional tag sets in the tool's xml with it? To
 suppress the unnecessary options for a given file type? or more than one?


It sounds like you want to use the conditional and param tags,
but rather than responding to another parameter directly (e.g. a select),
you want to look at an input file parameter's file type?

I don't know if that is possible, but I can thing of a couple of examples
where I could use that functionality.

Peter

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