Question: Environment variables in label field of output block?
gravatar for luke.turechek
19 months ago by
luke.turechek0 wrote:

Hi all, first post, but I'm hoping someone can help with the following issue I'm having:

I would like to be able to modify what ends up in the label field of an output block. Currently I have something like <outputs> <data format="fasta" name="trimoutputHC.fas" label="${}_HC" from_work_dir="outputHC.fas"/> </outputs>

However, I'd like to be able to break up the contents of $ I've managed to do that in an <environment_variable> block, and I've managed to echo those values in the command block, but Galaxy fails when I try to use them in the above context.

Does anyone have insight into the correct way to do this?

Any thoughts would be greatly appreciated, as this has me stalled at the moment.

Thank you! Luke

galaxy • 376 views
ADD COMMENTlink modified 19 months ago by Anton Nekrutenko1.7k • written 19 months ago by luke.turechek0
gravatar for Anton Nekrutenko
19 months ago by
Penn State
Anton Nekrutenko1.7k wrote:

Can you tell me why you need to do this? Perhaps there a simpler solution

ADD COMMENTlink written 19 months ago by Anton Nekrutenko1.7k

Hello Anton, I have multiple different fastq files which I am processing, and I am aggregating info about those files into a .csv sheet. I'm tracking the names of these samples through the label="" field in the output definition(s). But there doesn't seem to be a whole lot of flexibility around what you can put in that field. It would make my life a lot easier if I could more accurately specify what I want that field to look like as individual samples are run through different processing scripts.
I can work around this if I have to, but this would be the easiest way in my context (and I wouldn't have to do any jumping jacks in my Python code to get everything to play nicely.)

If it's just not set up for that, I can make it work, but if you have any thoughts, I'd really appreciate it. -Luke

ADD REPLYlink written 19 months ago by luke.turechek0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 167 users visited in the last hour