Hi guys,

The Tools API is currently working for me from galaxy-central, but I'm
not sure how to correctly run a tool. Are there any example scripts,
as there are for some other parts of the API? Specifically I want to
find out what the expected payload fields are when I post to CREATE to
run a tool.

Some of the fields are clear to me just from the api/tools.py code
(e.g. 'tool_id') but others are not (e.g. how the input datasets and
parameters are specified).

A separate question:

How do we specify "Advanced" or conditional-dependent fields for a
tool? Some of these fields are necessary to run the tool at all.
For instance, on my system, calling
    "description": "Find splice junctions using RNA-seq data",
    "id": "tophat",
    "inputs": [
            "html": "%3Cselect%20name%3D%22input1%22%3E%0A%3C/select%3E",
            "label": "RNA-Seq FASTQ file",
            "name": "input1",
            "type": "data"
            "label": "Conditional (refGenomeSource)",
            "name": "refGenomeSource"
            "label": "Conditional (singlePaired)",
            "name": "singlePaired"
    "name": "Tophat for Illumina",
    "version": "1.5.0"

This is obviously only some of the inputs you see in the UI. I think
that all the Advanced fields are missing, and more importantly, any
input which is dependent on a conditional is missing. So the
refGenomeSource conditional is there, but the actual reference genome
field is not. The type of the reference genome field also presumably
depends on which value is supplied for the referenceGenomeSource

Is there currently a way to specify (or see) these missing fields?



Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357          M: 0414 854 759
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