Without 'Available inputs are:' it is not possible to rename datasets in workflows?

Question: Without 'Available inputs are:' it is not possible to rename datasets in workflows?

3.3 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

I am trying to set up a workflow renaming each dataset in an informative manner using the #{} format described in
https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit?action=show&redirect=Learn%2FAdvancedWorkflow%2FVariables

However I see that the critical tool specific information about renaming is no longer shown with the renaming menu options .
Specifically the 'Available inputs are:' are no longer given.
Without this informationI cannot see how any users can use this critical function to write new workflows (the advice in the help-link assumes this information is available ).

Thanks Guy

Current -Usegalaxy.org for freebayes

Add Actions: 'output_vcf'
Rename dataset

This action will rename the result dataset. Click here for more information. (newname)

OLDERr -Usegalaxy.org for freebayes

Rename Dataset
on output_vcf
New output name:
Available inputs are: reference_source|input_bams_0|input_bam

PS does anybody know what the current 'Available inputs are:' for FreeBayes are? - bayesian genetic variant detector (Galaxy Tool Version 0.4)

workflow available inputs are #{} naming • 1.0k views

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modified 3.1 years ago • written 3.3 years ago by Guy Reeves • 1.0k

3.1 years ago by

Guy Reeves • 1.0k

Germany

Guy Reeves • 1.0k wrote:

Update

I thought I would mention that this matter has been resolved (including for users on usegalaxy.org)

https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit?action=show&redirect=Learn%2FAdvancedWorkflow%2FVariables

Though tools which take a variable number of files as an inputs appear to fail to take the name of any input file. Tools which I cannot personally get to name correctly are

Convert, Merge, Randomize 0.0.0.1 - using ‘Header' option
FreeBayes - even wen using single input BAM
Concatenate datasets tail-to-head (Galaxy Tool Version 1.0.0)

Thanks Guy

ADD COMMENT • link modified 3.1 years ago • written 3.1 years ago by Guy Reeves • 1.0k

Thanks Guy,

I am not sure if this is captured in another github ticket (perhaps as a suite of enhancements), but breaking it out might be helpful. It can always be linked back into any master enhancement tickets. Plus, the dev team will let you know in the issue comments how it is best organized. Create issue here: https://github.com/galaxyproject/galaxy

Jen

ADD REPLY • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen

I have created an issue

https://github.com/galaxyproject/galaxy/issues/1055

ADD REPLY • link written 3.1 years ago by Guy Reeves • 1.0k

3.3 years ago by

frederik.coppens • 40

VIB, Gent, Belgium

frederik.coppens • 40 wrote:

Hi Guy

The xml file for this tool can be found here: https://github.com/galaxyproject/tools-devteam/blob/master/tools/freebayes/freebayes.xml

Based on this file and the info you gave in the OLDER example, I would assume you need to use e.g. #{reference_source.input_bams_0}. This would then give you the name of the first bam file you provided (not sure if this will work though)

Frederik

ADD COMMENT • link written 3.3 years ago by frederik.coppens • 40

#Hi Frederik

Thanks a lot of the response but i tried #{reference_source.input_bams_0} but it does not work (at least for me). I looked at the .xml code myself but it is beyond me to figure out what will work.

Thanks for the help with the specific problem with this tool , but I still think there is a general problem with not having all the necessary info available.

Guy

ADD REPLY • link written 3.3 years ago by Guy Reeves • 1.0k

3.3 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k wrote:

I'm working on workflow actions today and will check into why your freebayes example isn't working. I'll update this post when I know more.

ADD COMMENT • link written 3.3 years ago by Dannon Baker ♦ 3.7k

Thanks so much. Guy

ADD REPLY • link written 3.3 years ago by Guy Reeves • 1.0k

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PS does anybody know what the current 'Available inputs are:' for FreeBayes are? - bayesian genetic variant detector (Galaxy Tool Version 0.4)

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