galaxyproject / galaxyproject/tools-iuc

iqtree: rcluster and rclusterf seem not to be optional

Open
#5,488 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
HTML
Stars
201
Forks
525
Avg merge
23h 54m
Merged PRs (30d)
59

Description

Admin of [usegalaxy.eu](https://usegalaxy.eu) here. I have seen this [report](https://sentry.galaxyproject.org/organizations/galaxy/issues/60110/events/efaa6db5a98643778006c0d6bf540ef7/) on our Sentry instance.

**tool_id**: toolshed.g2.bx.psu.edu/repos/iuc/iqtree/iqtree/2.1.2+galaxy2
**runtime**: CPython 3.11.5
**command_line**:
```shell
iqtree --prefix PREF -T ${GALAXY_SLOTS:-10} --redo -s '/data/******/******/******/******/dataset_********-****-****-****-************.dat' --seqtype AA -m 'MFP' --merge rclusterf --rclusterf --rcluster-max --msub 'nuclear' --cmin '2' --cmax '10' --merit 'AICc' --modelomatic --ninit '100' --ntop '20' --nbest '5' --nstop '100' --radius '6' --perturb '0.5' --polytomy --alrt '1000' --sup-min '0.0' --ufboot '1000' --boot-trees --nmax '1000' --nstep '100' --bcor '0.99' --beps '0.5'
```
**stdout**: ` `
**stderr**: `Expecting floating-point number, but found "--rcluster-max" instead`

I think the source of this error is [here](https://github.com/galaxyproject/tools-iuc/blob/c083399ddb31b026aaab1d600d8789bf56cf4d4b/tools/iqtree/iqtree.xml#L141-L146). If you check the documentation of [IQ-TREE](http://www.iqtree.org/doc/iqtree-doc.pdf#page=119), there seems to be no default value for `-rcluster` and `-rclusterf`. In addition, the docs [do not seem to imply that giving a value is optional](http://www.iqtree.org/doc/iqtree-doc.pdf#page=42). So I guess if either argument is passed, a value is needed.

The citation is also wrong. In the documentation, the fast relaxed clustering
algorithm (rclusterf) cites Lanfear et al., 2017, while the relaxed clustering algorithm (rcluster) cites Lanfear et al., 2014. However, the tool wrapper cites Lanfear et al., 2014 twice.

Contributor guide

Open the contributing guide

Research direction

Inspect tools/iqtree/iqtree.xml around lines 141-146 and compare the rcluster and rclusterf option definitions with the linked IQ-TREE documentation. Confirm how values are handled, correct the citation for rclusterf, and verify that the wrapper accepts the documented option forms without reproducing the reported command-line error.

Written by the indexing model from the issue text.

Assessment

Domain
cli, tooling
Issue type
Bug
Difficulty
2/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
55/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.