In my earlier email about Barcode/adapter/primer trimming/filtering of
sequences/reads I wrote:
> ...
>
> Currently I have used three separate scripts, with three separate
> XML files - one for each supported file type (FASTA, FASTQ, SFF).
> They all have the same interface, so could be done as a single
> XML wrapper. The only potential downside to that is that as written
> the SFF script requires Biopython, while the FASTA and FASTQ
> scripts currently use the Galaxy libraries instead. This external
> dependency may be an issue if Galaxy were interested in
> including this tool in the main distribution - or if I bundled this
> as a single tool or tool-suite on the Tool Shed.
>
> Any thoughts?

It occurred to me the same applies to three of my existing tools
in the Tool Shed:

* Filter FASTA by ID (uses Galaxy libraries)
* Filter FASTQ by ID (uses Galaxy libraries)
* Filter SFF by ID (uses Biopython)

They could be replaced by a single meta-tool supporting all
these file formats (and potentially more), say:

* Filter sequences by ID

On the one hand this modularity is useful if you don't want to
install all the dependencies and only need some of the file
formats, but they are conceptually doing the same task so it
just clutters the Galaxy tools menu even more if they get three
separate entries.

Assuming I did go ahead and merge the tools, does the Tool
Shed have any "obsoleted" or "deprecated" status, whereby
people could still download it (e.g. if it is being used in a
published workflow, not an issue here I don't think), but make
it clear that another tool is recommended in its place? I could
of course just update the description to say this in words.

Peter
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