None of the fixes are newer than that - and I haven't checked exactly
but I guess any applied to 15.07 had already been propagated back to
dev by August 4th. I would try to build the minimal example and hand
it off to me then - this really should work.

The size list thing is a bit awkward - is this just so you can use the
structured_like="" attribute on the output collection? I would just
use a dynamic output collection I guess with a discovered_datatsets
tag.

Merging collections should also be a native operation that doesn't
require a formal tool - along with other stuff like filtering
empty/bad datasets, zipping and unzipping pairs, splitting/merging
using operations defined on datatypes, etc.... I plan to throw
together a framework for collection operations (hopefully this next
release cycle).

-John

On Fri, Aug 7, 2015 at 6:58 PM, Aaron Petkau <aaron.pet...@gmail.com> wrote:
> Hello John,
>
> I tested this out on the github Galaxy with a commit from August 4
> (253ce7b8e3ddad7693da034374bed1a751173839) in dev.  Were any of the fixes
> you added done since then?  I'll try it out on the 15.07 release though.
>
> I would like to ask your opinion about something though.  So, the tool I'm
> trying to write is one to merge 2 dataset lists together into a larger list.
> The problem I want to solve is that we often deal with paired-end sequencing
> data (and collections work awesome for that), but not all sequencing is
> paired-end.  Sometimes we have single-end data as well we want to put
> through the same workflow.
>
> So, I figured I can just have another "input" element in my workflow for
> both paired-end and single-end.  The first step is reference mapping which
> produces BAM files.  I can do that separatly (since the mapper needs
> different parameters for single vs. paired end), but then I want to merge my
> BAM file lists together).
>
> That is, I have a workflow like:
>
> +--------------+       +---------------+
> |              |       |               |
> |  Paired-end  +------^+ Ref Mapping   +--------------+
> |              |       |               |              |
> +--------------+       +---------------+     +--------v--------+
>                                              |                 |
>                                              | Merge BAM Lists +------>
>                                              |                 |
> +--------------+       +---------------+     +--------^--------+
> |              |       |               |              |
> | Single-end   +------^+ Ref Mapping   +--------------+
> |              |       |               |
> +--------------+       +---------------+
>
> So, I was trying to develop a tool to merge both lists together.  I was
> doing this by writing a tool that takes as input both BAM lists, along with
> another list defining the exact size of the merged lists but with empty
> datasets, and copying any datasets over.  That is:
>
> Input List1: [A: a.bam ,B: b.bam]
> Input List2: [C: c.bam]
> Input Size List: [A: empty, B: empty ,C: empty]
>
> Output List: [A: a.bam, B: b.bam, C: c.bam]
>
> I know it looks a bit ugly to have that "size list" around, but I'm
> automating execution of the workflow so it's not as big of a deal to me.
> Not sure if you have any other solutions?
>
> Thanks for taking the time to read over this.  I'll do a bit more testing of
> my tool in other Galaxy versions.
>
> Aaron
>
> On Fri, Aug 7, 2015 at 12:15 PM, John Chilton <jmchil...@gmail.com> wrote:
>>
>> Aaron,
>>
>>   We fixed a few bugs related to this recently. Are you targetting
>> bitbucket or github - and which tag of Galaxy? I would probably target
>> the 15.07 release on github for the latest and greatest fixes.
>>
>>   If that still doesn't work I would recommend trying to pair down the
>> tool and workflow to build a minimal example to post. This really
>> should work in the abstract.
>>
>> -John
>>
>> On Fri, Aug 7, 2015 at 6:11 PM, Aaron Petkau <aaron.pet...@gmail.com>
>> wrote:
>> > Hey,
>> >
>> > So, I've been working on a tool which will product a new dataset
>> > collection
>> > as output.  I was following some of the instructions from
>> >
>> > https://bitbucket.org/galaxy/galaxy-central/pull-requests/582/allow-tools-to-explicitly-produce-dataset/diff.
>> > I managed to get the tool itself working, but when I go to use it in a
>> > workflow I'm getting errors.  Mainly:
>> >
>> > History does not include a dataset collection of the correct type or
>> > containing the correct types of datasets
>> >
>> > I'm wondering if there's something I'm doing wrong, or if tools which
>> > product dataset collections are not supported within workflows?  I'm
>> > working
>> > with the second case in that merge requests, using an input list as the
>> > structure for my output list.
>> >
>> > Thanks,
>> >
>> > Aaron
>> >
>> > ___________________________________________________________
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>
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