The “type” of the dataset collection created will matter for the data to show up on an input field, as well as the “datatype” of the data inside the collection, and the “content” of that data inside each dataset (this part doesn’t have a distinct metadata attribute – could be forward fastq reads, reverse fastq reads, or interlaced forward/reverse fastq reads). Collections are built up from those to create four options.
Many options … but maybe the explaination below will help.
- Four different content inputs variations are possible
- Three can be given as one of three different dataset types: individual files, multiple individual files, or a dataset collection that fits the overall entry type.
- One can be only given as a dataset collection (item 3 below).
- That translates to 10 different choices, just for the fastq input.
Screenshots, then I’ll explain what each can contain:
The four input “content” types for this tool (many will only have the first three but expect that to evolve over time as interlaced inputs are added to more tools):
The tool form changes dynamically based on the choice made.
The three dataset types available for the first two and the last from the list above are in the screenshots below. The declared “collection” will only accept a paired-end collection (so, you won’t see the options below for it - a collection is already expected).
Single-end: Single end sequences in each original individual dataset. Those can be entered as individual datasets, or selected as multiple datasets, or be put in a “list” type of dataset collection.
Paired-end: Paired-end sequences, forward in an original individual dataset and reverse in an original individual dataset. Those can be entered as individual datasets, or selected as multiple datasets, or be put into two distinct “list” type of dataset collections. One list for the forward, one list for the reverse.
Paired-end Dataset Collection: Paired-end sequences, forward and reverse added to a dataset collection that contains one pair of F/R reads or a combined “list of pairs” if you have more than one pair. The collection is created from data that has the forward reads in one or more datasets originally, each with a matching reverse read dataset).
Paired-end data from single interleaved dataset: Paired-end sequences, forward and reverse interleaved (interlaced) in an individual dataset (this is what you had/have, before “de-interlacing”). Those can be entered as individual datasets, or selected as multiple datasets, or be put in a “list” type of dataset collection.
Hope that helps!