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CPT's Galaxy Tools

License: GNU General Public License v3.0

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rhinogradentia guiwenting mdcarruthers choi-nakjun

galaxy-tools's Issues

spanin tool: add SD filter for both isp/osp

New Tool Request: MultiQC

This tool is on the EU Galaxy and is really nice for aggregating multiple fastQC files. It can do a lot more than that, but currently, the only way to aggregate such reports is to concatenate files, which creates redundant and useless data, so this tool should help with that on my assembly workflow and for future data analysis. This is the website of the tool, here is the github site and the toolshed link is here.

Add CRISPR-related tools into Galaxy

CRISPR-finder for finding repeats: http://crispr.i2bc.paris-saclay.fr/Server/
PHASTER for finding the proteins: http://phaster.ca/

Add InterPro link in popup window

When browsing hits in the InterPro Scan evidence track, can we add a direct link to the Interpro website with that IPR number in the popup window?

spanin tool: both need to require phage start

gbk information -> gff3 information? or just phage validator report

New Tool Request: Phigaro

Currently, most prophage detection programs can only be run using command-line interface. There are only 2 or 3 that can be done on other web servers. This particular tool takes raw genomic sequences, which will be very helpful for our current CF project. I placed two links to both the source code, and the paper describing how the program works.
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa250/582287
https://github.com/bobeobibo/phigaro

Spanin finder bug: SD on candidate O spanins is off

Galaxy login bug: null user loop

impersonate a user
log out
you now and will forever be a null user unless you clear your cookies again

delete reopen fasta sequences

Further development of genome mapping tools

We need good genome mapping tools. When someone can fit this in, the follow tools need to be tested and further developed.

(1) Our current genome mapper tool is crude and the output needs heavy editing in imaging software. It would be nice to refine the output so that the output can be more directly usable. When someone can fit this in, we can discuss the ideal output look.

(2) X-vis also need to be polished so that the output is more defined

(3) Circos tools (PSM prep and PSM plotter, PSM comparison table) need to be checked to see if they still function at all (there should have been at least some bug reports associated with these tools in the past several months)

interpro results invisible

Spanin finder/Apollo bug: I spanins don't display nicely

Public Repo out of sync with private repo

Somewhere the this repo got out of sync with our private Github Enterprise repo. Need to rebase and merge

blast result 0 -> low opacity result -> WRONG.

spanin tool: short lipoboxes

Adjacent genes tool

Karthik and I are studying the LydA-LydB holin-antiholin proteins of phage P1. These genes are always adjacent.
I need a tool that takes a protein record, finds the associated nucleotide record and then pulls the CDS (aa) sequence from the adjacent CDS, either upstream or downstream. Ideally it would ask for upstream or downstream and in the perfect world, ask how many adjacent CDSs to fetch. (i.e., 2 upstream, 3 downstream, maybe option for both.)

Need of course doesnt mean it is possible.

As I understand it there may be more than one nt record for a protein record but that is ok. It could just go to the top one, fetch the adjacent CDS according to spec, and then report the locus tag of the nt record accessed.

Convert PSM tools to python and simplify interfaces

instead of <repeat> blocks in prep, use <input multiple="True">
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