Yes! The dynamic_options parameter looks to be just the thing I was looking
for! Many thanks for pointing it out as it is missing from the wiki.
-AR
-Original Message-
From: Hans-Rudolf Hotz [mailto:h...@fmi.ch]
Sent: Tuesday, March 08, 2011 3:56 AM
To: Rodriguez, Aaron (NIH/NCI) [C]
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Referencing data library directly from tool's input
parameter dropdown.
On 03/07/2011 10:58 PM, Rodriguez, Aaron (NIH/NCI) [C] wrote:
Hello all. First of all thanks to Galaxy developers and supporters for this
great tool -- I'm experimenting with adding my custom tools to galaxy and
I'm very impressed with how simple galaxy makes this process.
Some of the tools that I'm adding to my local instance take reference files
as a parameter. These files are often large and fairly static. I
understand that I can create a data library where users can select the
reference file needed and import into history for analysis. However, I
would like to know if it's possible for a tool's input parameter (dropdown)
to enumerate these files from a public data-library (to avoid the steps
needed to import from library into history) and have that file pathname
become the value for my parameter?
As an alternative, would it be possible to load such a drop down from files
(of a certain type) existing at some predefined system path?
Hi Aaron
Our old trick with the dynamic_options attribute will probably work
for you as well (see also my reply to Populating tool select menu with
database data? I sent on February 8th to this list)
you can do something like:
inputs
param name=foo type=select label=what
help=Use tickboxes to select
display=radio
dynamic_options=ds_fileOptions()/
/inputs
outputs
/outputs
code file=extra_code_for_file_list.py /
help
/help
/tool
and then we have a little python script (extra_code_for_file_list.py)
with the ds_fileOptions function (I am not a python programmer, but I
managed to get it to work), which lists files ending with the
extension .ref
import os
import re
import operator
rDir = /path/to/my/referencefiles/
def ds_fileOptions():
l = os.listdir(rDir)
l.sort()
p = re.compile('[a-z]+\.ref$')
diroptions = [(s) for s in l if os.path.exists(rDir + s)]
dirs = [(s,s,False) for s in diroptions if p.match(s)]
return dirs
I hope this helps, Hans
Thanks in advance,
-AR
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