Question: Custom tool development: how to output multiple files to a directory?
gravatar for LF
3.5 years ago by
United States
LF10 wrote:

Hi all,

I am trying to implement a script into a galaxy server that I usually run on the command line.

The script produces a variable number of output files and saves those into an output directory that can be specified on the command line.

I found an article on the Galaxy wiki pages that describes this scenario:

However, I have further questions:

What's the best way to set up the output directory? When I try to generate it from within the script, it won't let me (probably actually a good thing for security reasons...!)

Can I run a mkdir command before calling my script? If yes, do I need to specify two <command> tags in the XML tool file? One for the shell mkdir command and one for calling the perl script? (<- I tried this but couldn't get it to work)

Thanks for any ideas!

development galaxy custom tool • 1.4k views
ADD COMMENTlink modified 3.5 years ago by Bjoern Gruening5.1k • written 3.5 years ago by LF10
gravatar for Bjoern Gruening
3.5 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

You can only specify one command tag until know, but there are discussions ongoing to support multiple in the future. But what you can do is simply putting as many shell commands together as you want in one tag. Please note to not use an interpreter, just a plain tag. For example see this one here:

Hope this helps,


ADD COMMENTlink written 3.5 years ago by Bjoern Gruening5.1k

Ok, that works -- thanks!!

ADD REPLYlink written 3.5 years ago by LF10
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