Hi Brad, What if its multiple file paths that the user types in rather than actual files, which makes it so the tool can't be executed in batch mode, would it still be workflow compatible at that point? Thanks for pointing me to the Bowtie wrappers as an example. Katherine
On Fri, Aug 26, 2016 at 10:45 AM, Langhorst, Brad Langhorst@neb.com wrote:
HI Katherine:
Multi-input/output should work fine…
You could have a look at the bowtie wrappers for an example.
It takes up to 2 fastq files and a reference. I can output a few files (unmapped, mapped, etc)
Brad — Brad Langhorst, Ph.D. Development Scientist New England Biolabs
On Aug 26, 2016, at 10:42 AM, Katherine Beaulieu < katherine.beaulieu014@gmail.com> wrote:
On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu < katherine.beaulieu014@gmail.com> wrote:
Hi Peter, I think I did not explain myself well. I meant that if I have a tool that takes multiple file paths and outputs multiple Galaxy datasets to the history, would this tool be workflow compatible, meaning capable of being a part of any workflow? From the behaviour I am getting now I am assuming it isn't but I just wanted to confirm that this isn't supported functionality.
On Fri, Aug 26, 2016 at 10:34 AM, Peter Cock p.j.a.cock@googlemail.com wrote:
Hi Katherine,
Are you asking about compatibility staying on the same Galaxy instance, or the harder problem of compatibility sharing workflows between Galaxy servers?
Taking data from input Galaxy datasets should be fine, anything else may not be portable. Even the relatively simple case of using datafiles referenced via an example.loc file (e.g. BLAST databases) would require the entries in the example.loc file be synchronised between Galaxy instances, and the associated data files too.
Peter
On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu katherine.beaulieu014@gmail.com wrote:
Hi Everyone, Would anyone be able to tell me the conditions which would make a tool non-workflow compatible? I have a tool that imports files from a third
party
application and auto-detects the file format. There is also the option
to
upload multiple files at once so the tool always uploads at least two
files.
From what I have described can anyone see why this tool would not be
able to
send one of its files to the next tool in the chain, ex. a text
manipulation
tool? Thanks, Katherine
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