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Question: Workflow variable rename not working
0
gravatar for tiagoantao
3.2 years ago by
tiagoantao • 30
United States
tiagoantao • 30 wrote:

Hi,

I use constantly dataset renaming in my workflows but I have a case where there might be a bug.

In the Abyss plugin I am renaming my scaffold output as:

#{reads1}.scaffolds

But it comes out renamed as

.scaffolds

(i.e, nothing is replaced)

I am suspecting that this might eventually be a galaxy bug.

For reference the .xml of the definition is here

I wonder if the variable name being inside a macro is a problem?

 
workflow abyss • 913 views
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modified 2.8 years ago by Brad Langhorst • 100 • written 3.2 years ago by tiagoantao • 30
2
gravatar for Brad Langhorst
2.8 years ago by
Brad Langhorst • 100
United States
Brad Langhorst • 100 wrote:

This has been migrated to github...

 
ADD COMMENT • link written 2.8 years ago by Brad Langhorst • 100
1
gravatar for Jennifer Hillman Jackson
3.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If this is intended to be a custom variable entered at run-time, then the variable is ${var}.

The #{var} is for capturing an input dataset's name and using it to rename the output. The dataset name can vary by tools, and many have this value listed at the top of the workflow "tool form" panel (far right, same panel where the renaming is performed). 

There are a few tools right now that have variable multiple inputs where the input dataset names are no longer explicitly available in the workflow editor. A restoration of this prior functionality is in progress. There wasn't a Trello ticket for it yet, but I just made one for users to track for updates: https://trello.com/c/zSGviZFb

If you really want to find the names, examine the wrapper .xml for the tool you want to rename from. A link for each tool into the Tool Shed where this can be easily visualized can be found at the top of a tool's form at the top upper right corner: "See in Tool Shed" from the "Options" menu.

Our apologies for the current inconvenience, Jen, Galaxy team

 

 
ADD COMMENT • link written 3.2 years ago by Jennifer Hillman Jackson ♦ 25k
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