Re: [galaxy-dev] How to count the number of Workflow steps?
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/ 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 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 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 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,
>>>
>>> ___
>>> 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/
>>>
>>
>>
>
___
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/
Re: [galaxy-dev] How to count the number of Workflow steps?
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 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 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,
>>
>> ___
>> 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/
>>
>
>
___
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/
Re: [galaxy-dev] How to count the number of Workflow steps?
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 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,
>
> ___
> 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/
>
___
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/
