Hi, I have a question related to this Galaxy threads: http://dev.list.galaxyproject.org/Populating-tool-select-menu-with-database -data-tp4139069.html
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 = jsonrpclib.Server('https://<myserver>/rmi-general-information-v1.json')
sessionToken = server.tryToAuthenticateForAllServices(<user>, <password>) projects = server.listProjects(sessionToken) experimentType = 'HT_SEQUENCING'
def getExperiments(): eList = [] experiments = server.listExperiments(sessionToken, projects, experimentType) for experiment in experiments: eList.append([experiment['code'], experiment['code'], False])
return eList The corresponding XML file calls the getExperiments() function:
<inputs> <param name="experiment" type="select" label="Experiment:" help="select Experiment" dynamic_options="getExperiments()"/>
<outputs> <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:
*Experiment1 - Sample1 + fastq1.gz + fastq2.gz + fastq3.gz - Sample2 + fastq1.gz + fastq2.gz *Experiment2
- Sample1 + fastq1.gz
I am on Galaxy r7148. If somebody could direct me in the right direction would be highly appreciated.
Kind regards
Manuel
-- 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
