Galaxy Tool API - how to submit a non-specific file reference

Question: Galaxy Tool API - how to submit a non-specific file reference

2.5 years ago by

eric • 0

UC Berkeley

eric • 0 wrote:

I'm generally able to submit a Galaxy job through the API (POST /api/tools) where the input is a specific history reference to a file (in this case below, it's a FASTA file reference history element.)
But, how do I submit a non-specific reference, such that it would pickup the last available FASTA history element?

{
  "tool_id":"toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0",
  "tool_version":"1.2.0",
  "history_id": "f597429621d6eb2b", 
  "inputs":{
    "input_query":{
      "batch":false,
      "values":[
        {                       // history element of the file (this works)
          "hid": args.hid,  // ie "219"
          "id": args.id, // ie. "6000239ca29982"
          "name": args.name, // ie "myfile.fa"
          "src":"hda"
        }
      ]

    },
    "source_select":"13apr2014-htgs", // db select
    "word_size":"28",
    "iden_cutoff":"90",
    "evalue_cutoff":"0.001",
    "filter_query":"yes"
  }
};

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modified 2.5 years ago • written 2.5 years ago by eric • 0

2.5 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

I'm not sure why you'd ever want to do that, just automatically using the last reference. Can you explain the use case here a bit more?

What you might be looking for is the build endpoint:

GET /api/tools/<tool_id>/ should provide options, which you would then specify in a later request.

Try (when logged in) something like https://usegalaxy.org/api/tools/random_lines1/build for concrete details.

ADD COMMENT • link written 2.5 years ago by Dannon Baker ♦ 3.7k

Thanks for the response. Well, I suppose the way I wanted it to operate was the way I see it operate upon executing a tool from the GUI, where the default input is based on the defined input format, and last file generated entry of that format. However, I admit I'm rather new at the API and perhaps there are better ways of addressing it.
What I wanted to do is to queue up a series of tools that were whose inputs were dependent on some prior set of outputs, somewhat like a workflow, but not using workflows. And, these were queue by another application, namely JBrowse.

ADD REPLY • link written 2.5 years ago by eric • 0

2.5 years ago by

eric • 0

UC Berkeley

eric • 0 wrote:

Oh, I see how that works now. I can pass history references as inputs to tools and queue them up in advance. Each tool will not execute until the input from another history element's output is ready.

ADD COMMENT • link written 2.5 years ago by eric • 0

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