I have a question related to this Galaxy threads:

I implemented the example with the deprecated <code> tag which is working
fine. But I do not invest time in a tag which might vanish soon. What is
the replacement for this tag or how is the way it should be done?

Here is what I want to do:
My ultimate goal is to load fastq.gz files from an external Data
Management System which I can connect via a JSON API. Here is the code
which generates the menu shwon in the attached screen shot:
Python code:

import jsonrpclib
server = 

sessionToken = server.tryToAuthenticateForAllServices(<user>, <password>)
projects = server.listProjects(sessionToken)
experimentType = 'HT_SEQUENCING'

def getExperiments():  eList = []
  experiments = server.listExperiments(sessionToken, projects,
  for experiment in experiments:
    eList.append([experiment['code'], experiment['code'], False])

  return eList
The corresponding XML file calls the getExperiments() function:

  <param name="experiment" type="select" label="Experiment:"
  help="select Experiment"

  <data format="fasta" name="output" label="more foo" />

</outputs>   <code file="openbis_get_dataset.py" />

Depending on the selection in the first drop down list (experiments) I
want to show/fill a second list which shows a list of items which are in
the selected experiment. Finally the fastq files should be listed. The
structure is like this:

  - Sample1
    + fastq1.gz
    + fastq2.gz
    + fastq3.gz
  - Sample2
    + fastq1.gz
    + fastq2.gz

  - Sample1
   + fastq1.gz

I am on Galaxy r7148.
If somebody could direct me in the right direction would be highly

Kind regards


Manuel Kohler
Center for Information Sciences and Databases (C-ISD)
Department of Biosystems Science & Engineering (D-BSSE)
ETH Zurich, Maulbeerstrasse (1078, 1.02), CH-4058 Basel, +41 61 387 3132

<<attachment: Screen shot 2012-07-25 at 3.10.18 PM.png>>

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