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 http://localhost:8080/api/tools/tophat?key=.... returns { "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 conditional. Is there currently a way to specify (or see) these missing fields? Thanks, Clare -- 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
