Add library-wise logic to atlas-fastq-provider wrapper

[pmb59]

Description

Make some refinements to the atlas-fastq-provider galaxy wrapper. ISL uses the library-wise downloader rather than file-wise, we need an extra option in the wrapper for that.

Basically, the wrapper needs a library-wise logic that calls fetchEnaLibraryFastqs.sh (if library-name param is provided) or fetchFastq.sh (if filename param is provided). Depending on each case, specific set of parameters need to be displayed.

This PR is related to ebi-gene-expression-group/atlas-fastq-provider#17

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Fixes # (issue)

Type of change

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Checklist

• I have made any required changes to upstream dependencies for a tool wrapper, and they are available in distribution channels (e.g. Pip, Conda).
• If I have updated the underlying software for a tool wrapper (e.g. scanpy-scripts by changing the value of @TOOL_VERSION@), then I have reset all 'build' values to 0 (e.g. @TOOL_VERSION@+galaxy0)
• If I have updated a tool wrapper without a software change, then I have bumped the associated 'build' values (e.g. @TOOL_VERSION@+galaxy0 @TOOL_VERSION@+galaxy1)

[pmb59]

@pcm32 We need to bump atlas-fastq-provider to 0.4.3 and deploy in a new conda version before this will work.

Also we might need to add:

• a conditional to the outputs based on main_source (lib or file)
• a new test for main_source="library"

[pcm32]

I guess we are waiting for the bump here, correct?

[pcm32]

Some comments to improve this.

[anilthanki]

@pmb59 and @irisdianauy can you please add couple of tests utilising Resources and directory and Retrieval Method options.

[pcm32]

Some minor comments

[anilthanki]

LGTM

[pmb59]

Thanks @irisdianauy and @anilthanki As all requests by @pcm32 are done, we are ready to merge.