"Input data" parameter for the SPAdes workflow element

Add a new parameter "Input data" for the "Assemble Reads with SPAdes" workflow element.

Parameter description

The parameter should have the following description:

Select the type of input for SPAdes. URL(s) to the input files of the selected type(s) should be provided to the corresponding port(s) of the workflow element.

At least one library of the following types is required:
* Illumina paired-end/high-quality mate-pairs/unpaired reads
* IonTorrent paired-end/high-quality mate-pairs/unpaired reads
* PacBio CCS reads (at least 5 reads coverage is recommended)

It is strongly suggested to provide multiple paired-end and mate-pair libraries according to their insert size (from smallest to longest).

Additionally, one may input Oxford Nanopore reads, Sanger reads, contigs generated by other assembler(s), etc. Note that Illumina and IonTorrent libraries should not be assembled together. All other types of input data are compatible.

It is also possible to set up reads orientation (forward-reverse (fr), reverse-forward (rf), forward-forward (ff)) and specify whether paired reads are separate or interlaced.

Illumina, IonTorrent or PacBio CCS reads should be provided in FASTQ format.
Illumina or PacBio read may also be provided in FASTA format. Error correction should be skipped in this case (see the "Running mode" parameter).
Sanger, Oxford Nanopore and PacBio CLR reads can be provided in both formats since SPAdes does not run error correction for these types of data.

Value in the Property Editor and the dialog

Show a placeholder "Configure input type" and a browse button ("...") in the "Input data" field in the Property Editor. Show a custom dialog on the browse button click (see the attached layout). The dialog title should be "Configure SPAdes Input Type".

Input ports and slots

Depending on the checkboxes selected in the dialog, add or remove the corresponding input ports. Thus, the following options are available:

1. "Input paired-end reads" with slots "Input URL 1" and "Input URL 2". Use the same IDs as in the "SPAdes data" port of the current version of the SPAdes workflow element, so that workflow with old SPAdes versions can be opened.
2. "Input mate-pairs" with slots "Input URL 1" and "Input URL 2"
3. "Input high-quality mate-pairs" with slots "Input URL 1" and "Input URL 2"
4. "Input unpaired reads" with slot "Input URL"
5. "Input PacBio CCS reads" with slot "Input URL"
6. "Input PacBio CLR reads" with slot "Input URL"
7. "Input Oxford Nanopore reads" with slot "Input URL"
8. "Input Sanger reads" with slot "Input URL"
9. "Input trusted contigs" with slot "Input URL"
10. "Input untrusted contigs" with slot "Input URL"

Running SPAdes

Use a YAML configuration file for specifying parameters to SPAdes.
Note that "PacBio CCS reads" have the same type "single" in the file (find out how the following scenario should be handled: input Illumina unpaired reads + PacBio CCS reads).

Default value and back compatibility

By default Illumina paired-end reads port should be added. Make sure a workflow with old versions of the SPAdes element can be opened.

Validation of required input

If none of the required input is not set, show the following error message on the element validation:

At least one of the required input ports should be set in the "Input data" parameter.