update naming of output for planemo run with --download_outputs

[Smeds]

When you run Planemo and request the output to be downloaded, the resulting files can be somewhat difficult to interpret. For example, executing the workflow available at https://iwc.galaxyproject.org/workflow/tissue-microarray-analysis-main/ produces the following files:

ls output_folder/
1__b2552ac3-3f9c-47ab-81d2-41e745b93cc4
'ASHLAR on data 4, data 8, and others__6a19612f-8782-4c09-9e6e-1e928f136696'
'BaSiC Illumination on data 2 DFP__9c965e55-91eb-4375-ad47-7449ec9f771f'
'BaSiC Illumination on data 2 FFP__bbf3f43c-d638-4b31-ba93-261c3201d98b'
'Convert image format on data 13__8d80d2a8-2dc7-4125-a473-8fb499b7cc45'
'Convert McMicro Output to Anndata on data 19__e7e3203f-b1ae-4363-b96d-de2f38046b9f'
'Perform segmentation of multiplexed tissue data on data 13 Mask__29a8d7a0-d7fa-4a7f-bc12-72deff4f42f0'
'Primary Mask Quantification__b768b992-a7fb-45b4-b0bc-692e843a0e3a'
'Rename OME-TIFF channels on data 4 and data 17__86d59586-58c7-484c-96bf-36f0740e0e63'
'Single Cell Phenotyping on data 1 and data 23__d3a7d97c-031a-49a6-8788-8cc7c6a840d4'
'UNetCoreograph on data 9 TMA Map__26b2c36e-7ae1-4171-a54b-8bd287e6bde6'
'Vitessce on data 25, data 15, and data 21__4a443f3a-a3a8-4ea4-86f9-1c5496b08482'

None of the downloaded files include file extensions, which makes it difficult to know how to open them—especially if you're not already familiar with how the workflow is constructed.

I would like to see:

File extensions

That extensions are added

2 Simple name

The current approach, where the task or job name is included in the filename, results in long and hard-to-read filenames. I also find the use of spaces frustrating, as it causes quotes to be added around the filename. Would it be possible to introduce a customizable naming template for downloaded files?

[mvdbeek]

File extensions are easy, we should definitely do that.

task or job name is included in the filename, results in long and hard-to-read filenames.

You could perhaps create folders for the steps that produced the output ?

I also find the use of spaces frustrating, as it causes quotes to be added around the filename.

that's up to your shell, I'm not sure I would change this.