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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