On 7 Dec 2017, at 6:59 pm, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:

Hi Steve

what happened, when you add this module to the environment the galaxy server is running in? (e.g. by listing the path in the 'run.sh' file)

Regards, Hans-Rudolf


On 12/07/2017 03:05 AM, Steve Cassidy wrote:

Hi all,
  this would help in a tool I’m trying to write too but the problem I
have implementing this approach is that my script will need an external
python module - is there any way that I can list dependencies for the
script?  As it happens these are the same dependancies that the tool
itself will need once executed.

Thanks,

Steve

—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

On 24 Nov 2017, at 6:52 pm, Hans-Rudolf Hotz <hrh@fmi.ch
<mailto:hrh@fmi.ch>> wrote:

Hi Evan

Yes, this is possible with "dynamic_options"

e.g.:

<tool ...

<inputs>

<param name="year" type="select" label="from which year"
   display="radio" refresh_on_change="true" >
            <option value="/2017" selected="true">2017</option>
    <option value="/2016">2016</option>
            <option value="/2015">2015</option>
</param>

<param name="file" type="select" label="select a run"
  display="radio"
  dynamic_options="ds_readFiles(year)"/>


</inputs>
<outputs>
...
</outputs>
<help>
...
</help>
<code file="more_code.py" />

</tool>

The python function "ds_readFiles" is defined in a extra code file
"more_code.py", which is stored in the same directory as the tool
definition file. The function returns all files with a matching file
name (i.e.year), and could look like:


rDir = "/data/"

def ds_readFiles(year):

  l = os.listdir(rDir)
  p = re.compile('^%s_[0­9]{4}_M[0­9]{5}_[0­9]'%year)
  l.sort()
  path = rDir
  filesoptions = [(s) for s in l if os.path.exists(path + s)]
  files = [(s,s,False) for s in filesoptions if p.match(s)]
  return files



a similar case is also described here:

http://dev.list.galaxyproject.org/Dynamic-Tool-Parameter-Lists-td4175828.html


Hope this helps, Hans-Rudolf


On 11/23/2017 06:02 PM, Evan Clark wrote:

Is it possible to execute a script within a tool xml confit to retrieve
some data and append to the ui depending on the requested data. I.e if I
wanted to get a list of files and provide them as select options before
hitting the execute button.


---
Sent from VMware Boxer


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