Greg Von Kuster

Add DRAM data manager and set db locations tools

10

FOR CONTRIBUTOR: * [x] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [x] - License permits unrestricted use (educational + commercial)...

Add the gtdbtk_classify_wf tool

1

FOR CONTRIBUTOR: * [x] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [x] - License permits unrestricted use (educational + commercial)...

Add the data_manager_gtdbtk_database_installer tool

3

FOR CONTRIBUTOR: * [x] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [x] - License permits unrestricted use (educational + commercial)...

planemo uploads to the Tool Shed include unwanted files

4

It seems planemo is uploading unwanted files to the Tool Shed with individual tool uploads. In some cases it uploads multiple tools from a demultiplexed git repository into a single...

DRAM database config should be accessible / configurable by users

2

The DRAM database config file is restricted from users - it is written and maintained fully within the DRAM code (e.g., https://github.com/WrightonLabCSU/DRAM/blob/a5f225718c5ff312ec8ccaefbb61daaa12452705/mag_annotator/database_handler.py#L28-L33). Storing / maintaining the config file in the...

DatabaseHandler - missing database should raise an exception

1

In the DatabaseHandler, if the database is missing, a warning message is printed (https://github.com/WrightonLabCSU/DRAM/blob/master/mag_annotator/database_handler.py#L46-L51) but processing continues and ultimately status code 0 is returned from the caller upon exit, so...

FOR CONTRIBUTOR: * [x] - I have read the [CONTRIBUTING.md](https://github.com/galaxyproject/tools-iuc/blob/master/CONTRIBUTING.md) document and this tool is appropriate for the tools-iuc repo. * [x] - License permits unrestricted use (educational + commercial)...

Planemo test should not require the use of the Galaxy upload tool

6

The primary process that planemo uses to test a Galaxy tool is to upload the tool inputs to the specified Galaxy test instance using the Galaxy upload tool. At least...

Fix for flye keep-haplotypes flag

1

Moved lines are planemo lint fixes, so not sure if they are necessary in this repo.

Please add DADA2-formatted reference databases to test/main

12

The dada2 tools are currently installed on Galaxy test and will soon be installed on Galaxy main. Please add the dada2 reference datasets https://benjjneb.github.io/dada2/training.html so that the tools that require...