Renaming files in a collection for BiG-SPAPE to avoid errors

[jennaj]

There are a few parts here so I’m going to number

1. Dataype

For this part

@Shreyash_04

I attempted to change the datatype to .gbk in the configure output for genebank files of antiSMASH. However .gbk is not available as a option.

I should have been more clear here

@jennaj

The tool form does use the datatype to detect inputs in select lists. So, both the correct filename.gbk and datatype genbank are needed for a successful run.

Name the file

filename.gbk

and assign (or leave?)

datatype assigned as genbank.

2. “Filename” of the inputs

@Shreyash_04

The rename function also did not workout. The main Output collection was renamed while the files inside the collection remained unchanged.

Correct, sorry.

The “filename” in a collection is a different attribute. Those are called the Element Identifiers, and sort of works like a file name. I just tested to see if modifying those was enough to get the tool to accept the renaming, and it did.

Instead of typing out how to do this, I’m going to share some Galaxy artifacts.

• original testing history https://usegalaxy.eu/u/jenj/h/test-bigscape

Then I created a small workflow with example manipulation steps, along with a rerun, and what resulted. This is what you can add to your workflow, or you can adapt mine.

• workflow https://usegalaxy.eu/u/jenj/w/relabel-test-bigscape
• using the original history as a source of inputs to the workflow, this is the output sent to a new history https://usegalaxy.eu/u/jenj/h/relabel-test-bigscape

Many more text manipulations tools are in these tutorials https://training.galaxyproject.org/training-material/search2?query=olympics and the workflow manipulations are in the workflow tutorials, and you can see the function used in other contexts in at least two other tutorials (see the bottom of the Relabel identifiers tool form).

Hope this is the solution but please review and try it out