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/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 rp...@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.ba...@gmail.comwrote:
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 rp...@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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[galaxy-dev] How to count the number of Workflow steps?
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/
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 rp...@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,
___
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 dannon.ba...@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 rp...@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,
___
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/
