Jeremy wrote:
> Peter wrote:
>> Any thoughts from the Galaxy team? Are you open to making
>> extract/extract_genomic_dna.xml more general - for instance
>> renaming and rewording to indicate work on protein FASTA
>> files as well as nucleotide FASTA files and reference genomes
>> (assuming it does work)?
>
> Peter,
>
> We're open to enhancing this tool. Here are my thoughts:
>
> *Enabling the tool to work with general tabular formats would
> seem to be a relatively low priority because it's easy to convert
> a general tabular file into a simple BED file by cutting columns.

For some of the example use cases I have in mind, I'd first
have to generate a start column of ones (beginning of the
sequence), and an end column of the length of the sequence.
But yes, I can see how this could be done.

> If you plan to support a general tabular format, the GOPS
> tools provide examples of how to work with BED, GFF,
> and interval datasets.

Putting GOPS into the Galaxy tool search brings up the
Operate on Genomic Intervals section, is GOPS short
genomic interval operations?

> *The tool should work with general fasta files right now,
> so the changes needed to support protein and other
> fastas should be UI-based only.

Right, while of course preserving the (now misleading) tool
ID of  "Extract genomic DNA 1" and filename of
extract/extract_genomic_dna.xml for backwards
compatibility.

I'll take a look at this then - thanks,

Peter
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