Question: Without 'Available inputs are:' it is not possible to rename datasets in workflows?
2
gravatar for Guy Reeves
3.0 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

HI

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)

ADD COMMENTlink modified 2.8 years ago • written 3.0 years ago by Guy Reeves1.0k
2
gravatar for Guy Reeves
2.8 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k 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 COMMENTlink modified 2.8 years ago • written 2.8 years ago by Guy Reeves1.0k

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 REPLYlink written 2.8 years ago by Jennifer Hillman Jackson25k
1

Thanks Jen 

I have created an issue 

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

ADD REPLYlink written 2.8 years ago by Guy Reeves1.0k
1
gravatar for frederik.coppens
3.0 years ago by
VIB, Gent, Belgium
frederik.coppens40 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 COMMENTlink written 3.0 years ago by frederik.coppens40
1

#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 REPLYlink written 3.0 years ago by Guy Reeves1.0k
1
gravatar for Dannon Baker
3.0 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k 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 COMMENTlink written 3.0 years ago by Dannon Baker3.7k

Thanks so much.  Guy

ADD REPLYlink written 3.0 years ago by Guy Reeves1.0k
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