tools-iuc

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@FMG0411 working on integrating the tool as part of his thesis.

SaimMomin12

Updating tools/virheat from version 0.7.1 to 0.7.4

3

Hello! This is an automated update of the following tool: **tools/virheat**. I created this PR because I think the tool's main dependency is out of date, i.e. there is a...

gxydevbot

Updating tools/amrfinderplus from version 3.12.8 to 4.0.23

6

Hello! This is an automated update of the following tool: **tools/amrfinderplus**. I created this PR because I think the tool's main dependency is out of date, i.e. there is a...

gxydevbot

samtools_depth should map over datasets

1

The `samtools_depth` treats a dataset collection as many bams. I think this not really standard usage of `samtools depth` which is (I think) performed on individual bams separately. This wouldnt...

ammaraziz

https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets NCBI Datasets Genomes tool fails on use with "unknown field 'assemblyMethod'": ```   -- Assembly BioSample BioProject Accession dataformat doesn't recognize this input For best results 1. Make sure to...

crashfrog

Update kraken-related tools to enable use of both Kraken and Kraken2 indexes

2

- [ ] tool_id toolshed.g2.bx.psu.edu/repos/iuc/bracken/est_abundance/2.9+galaxy0 - [ ] toolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-mpa-report/1.2.4 Braken pulls in Kraken indexes, but not Kraken2. Same for the mpa tool. Not sure of the exact status, but I...

jennaj

Usage issues with downloaded snpeff 5.N databases ORG and EU

2

The download tool is not downloading versions of the database that are compatible. Is there something we can do to make the usage clearer to users? Or can these tool...

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...

jennaj

hechth

Hello, I don't know if the issue is the tool wrapper or galaxy. I used the data_manager 'data_manager_fetch_genome_dbkeys_all_fasta' version 0.0.5. And the datamanager populates the table all_fasta.loc but not the...

lldelisle