One tool per file format, or one flexible tool?
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
Hello Peter, The idea of altering the description is perhaps best, since you want to rename into a new merged tool. If the names were the same, then uploading a new version would tag the prior as "Status = archived". Linking many-to-one for an updated version, across new tool names, is not currently an option. Hopefully this helps, Jen On 2/3/11 5:57 AM, Peter Cock wrote:
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.
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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org
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