Hello!
I’m trying to use these three dataset collections I got from the output of Slamdunk as the input for Alleyoop.
However, these do not show up in the list of options when selecting dataset collections.
I’ve tried selecting the files individually (for example, for the bam files:
but the files do not show up. Any ideas on how to fix this or what else I can try?
Thanks!
Welcome @pizzabytes
Hopefully you have discovered how to select a collection from the history on a tool form by now, but if now, I can try to explain now.
When ... browse/upload files is used, the base “shape type” still needs to be set. Since the data is in a collection, the collection folder icon would need to be selected first, before using the pull-down menu (sometimes easier) or the ... browse/upload function.
Screenshot Tool form select area with the collection folder icon highlighted and instructions to select it first, to inform the tool to expect that type of data shape.
My guess is that the multiple-file option was still selected instead (the default), then you clicked on the collection in the browse function, and because those shapes didn’t align, nothing happened. This could be trapped better with a warning about why the selection failed. I’ll ticket this for the developers.
Please give this a try if you haven’t already and let us know what happened in any case!
Apologies for our late reply! Our team of scientist is in an out over the summer and your question was difficult. But we can follow up now if you haven’t solved this! 
Hi!
Thank you for your response!
I tried this and I was able to select the files separately within the collection, but the collection itself as a whole is still not in the dop down list. For example, I want to select item 566 “Slamdunk on collection 468: BAM” but the only collection that shows up in the list is item 303. The only thing different between item 566 and 303 is that 506 is a list of pairs, while 303 is a list of single BAM files.
I was just testing the use of pairs vs single end reads so I was curious whether Alleyoop behaved differently, so perhaps this is less of a form issue and more of compatibilty with Alleyoop specifically?
I am now able to select the files I wasn’t before, so thank you so much for your help!
OK, thanks for explaining more, the screenshots really help!
The difference is probably between the pair and list type of collection formats. This tool seems to only want a list. There are two choices:
You can use the tool Flatten Collection to convert to a list format where both forward and reverse data are all in the same list collection together. The “forward” and “reverse” notation is added to the collection element names. These can be split out again by using Extract element identifiers, manipulating that text file with a text manipulation filter tool, then Filter collection.
The other way is to use Unzip collection. This creates two new list collections, one forward, one reverse. These can be combined again with Zip collection.
Your choice! There can be reasons to use both. Either of these would probably work to help the tool to “see” the data. And, interesting to test if it this protocol can handle paired-end data! I don’t know but you should be able to run some tests and compare results to learn about what may pop out, and sometimes that is the “truth” for practical purposes.
In summary for the technical parts: collections are like folders, there are a few different shapes, and you can convert between these. The data files inside are clones of the original files and don’t expand your quote usage, so feel free to experiment. Most of the tools you would use for changing collection folder shapes are in the tool panel in the Collection Operations section. The tools have simple help on each and a link to the full tutorial with examples at the bottom in the Help section. Any questions or you get stuck, please ask and we’ll try to help more here. 
