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.beaulieu...@gmail.com<mailto:katherine.beaulieu...@gmail.com>> wrote:



On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu 
<katherine.beaulieu...@gmail.com<mailto:katherine.beaulieu...@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.c...@googlemail.com<mailto:p.j.a.c...@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.beaulieu...@gmail.com<mailto:katherine.beaulieu...@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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