No, rename is a completely separate and unrelated action. Back to your original question, for counting the number of steps, can you just look at the api/workflows/<id> and look at the steps dict? Anything with a tool_id is a tool step. -Dannon On Tue, Mar 5, 2013 at 10:52 PM, Richard Park <rpark@bu.edu> wrote:
Hi Dannon, Thanks for the response. If there is a "RenameDatasetActionoutput_file" post job action, does that implicity mean that all other output files are considered HideDatasetActions? thanks, Richard
On Tue, Mar 5, 2013 at 6:36 PM, Dannon Baker <dannon.baker@gmail.com>wrote:
Manually adding "HideDatasetActions" via the right panel in the editor was deprecated a while back in favor of the workflow output 'asterisks' you see rendered on each step in the workflow editor, but they're still used behind the scenes. When you flag a step as an output, all other non-output steps should have HideDatasetActions added to the step automatically.
-Dannon
On Tue, Mar 5, 2013 at 5:32 PM, Richard Park <rpark@bu.edu> wrote:
Hi everyone, Does anybody know how Galaxy currently determines which outputs from a tool are shown when a workflow is run? I'm currently dynamically creating workflows based on the number of given inputs and iterating through all "HideDatasetAction*" for each tools "post_job_actions" to figure out the total number of steps that will be run.
"post_job_actions": { "HideDatasetActionoutput": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output" }, "HideDatasetActionoutput_suppressed_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_l" }, "HideDatasetActionoutput_suppressed_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_suppressed_reads_r" }, "HideDatasetActionoutput_unmapped_reads_l": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_l" }, "HideDatasetActionoutput_unmapped_reads_r": { "action_arguments": {}, "action_type": "HideDatasetAction", "output_name": "output_unmapped_reads_r" } },
In the latest galaxy, there no longer seems to be any "HideDatasetAction*" in each tools "post_job_actions" options. How does Galaxy know which output files for a tool it should show or process?
Does it have to do something with "RenameDatasetAction*"?
"post_job_actions": { "RenameDatasetActionoutput_file": { "action_arguments": { "newname": "19_output_file" }, "action_type": "RenameDatasetAction", "output_name": "output_file" } },
Any guidance would be much appreciated. Thanks,
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