Enhancement: enable rnaQuast to access the same native genome indexes as RNA-Star

[jennaj]

tool_id toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.3.0+galaxy0 toolshed https://toolshed.g2.bx.psu.edu/view/iuc/rnaquast/f73ab5187eed

The development repo points to a protected gitlab, so I'm hoping this is the correct place to post the request issue!

This tool is included in an updated GTN tutorial at this step: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/differential-isoform-expression/tutorial.html#transcriptome-quality-assessment-with-rnaquast

While the tutorial is using a custom reference genome, many users performing analysis will be using the built-in RNA-Star reference indexes. Up until this point, the native server genome index is used for all steps, then people are getting stuck.

Would it be possible to update the tool form to access the server's all_fasta.loc file? This would be the same base genome index as used with RNA-Star.

The option should be ? undefined for the default setting since some uses will not include a genome assembly. The toggle would have the choices as: none, server, history.

Workaround for end-users

1. The indexes included with RNA-Star can usually be accessed from the CVMSF resource located at http://datacache.galaxyproject.org/.
2. Some may be found here http://datacache.galaxyproject.org/indexes/ and others here http://datacache.galaxyproject.org/managed/.
3. If you cannot locate your index, you can ask for help!

Example: Human GRCh38/hg38 is at http://datacache.galaxyproject.org/indexes/hg38/seq/hg38.fa

• You can paste this URL into the Upload tool to get it into your history.
• The original source was from UCSC as described in https://help.galaxyproject.org/t/reference-genomes-at-public-galaxy-servers-grch38-hg38-example/11616
• The paired reference annotation can be sourced from UCSC at https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/ or from Gencode at https://www.gencodegenes.org/human/ (don't forget to remove the # header lines!)
• Getting all of your reference data at the very start of an analysis and using the same reference genome and reference annotation throughout the same analysis is recommended!

Reported at https://help.galaxyproject.org/t/issue-with-rnaquast-tool/15408/7