I am trying to combine paired-end data into a collection for use in the tool: Stacks: de novo map the Stacks pipeline without a reference genome (denovo_map.pl) (Galaxy Version 1.46.0). I uploaded the files individually and tried creating a collection a few ways.
First, I selected all files (24) and created a “list of pairs.” This seemed to work well (it created a list of 12 pairs), but I cannot get the Stacks: de novo map tool to recognize this list as a valid type of input.
Next, I tried to build a collection using rules, but could not figure out how to pair the files, so it ended up creating a list of 24 files. The tool recognized this collection, but I didn’t want to proceed without pairing the data.
Finally, I tried selecting each pair of files, building a dataset pair for each, and then combining these into a collection…but apparently you cannot build a collection from lists of data?
So, my questions are:
- Is there a Collection operation I need to use in order to proceed using the “list of pairs?” One that will make the tool recognize the list as a valid collection to input?
- Is there a way to pair files when building a collection from rules?