[Descriptor Issue]: Mrtrix3's mrdegibb axes parameter

[kaitj]

Package

MRTrix3

Tool Name

mrdegibbs

Problem Description

Separator for the axes parameter is currently white-space. Arguments should be comma-separated, otherwise additional values get interpreted as additional arguments to the command.

Steps to Reproduce

Run mrdegibbs with axes argument.

Logs

No response

[nx10]

Do you know if this one is auto-generated or one of their python apps? #238 will help make this clear in the future

[kaitj]

I think this one is generated form source code

[nx10]

Right, here is the json dump

niwrap/extraction/mrtrix/json_docs/reference/commands/mrdegibbs.json

Lines 38 to 52 in 50184d4

	{
	"id": "axes",
	"description": "select the slice axes (default: 0,1 - i.e. x-y).",
	"optional": true,
	"allow_multiple": false,
	"arguments": [
	{
	"id": "list",
	"description": "",
	"type": "int seq",
	"optional": false,
	"allow_multiple": false
	}
	]
	},

I wonder if their int seq type is always comma separated.

Edit: looks like our conversion script is guessing based on description

niwrap/extraction/mrtrix/mrt2bt.js

Line 186 in 50184d4

const comma_separated = option.description.includes("comma-separated");

[kaitj]

I think so - I can check in a bit, but something like dwi2response, also has a list of ints for lmax I think, which should be comma-separated.

[kaitj]

niwrap/extraction/mrtrix/json_docs/reference/commands/dwi2fod.json

Lines 133 to 143 in 50184d4

	"id": "lmax",
	"description": "the maximum spherical harmonic order for the output FOD(s).For algorithms with multiple outputs, this should be provided as a comma-separated list of integers, one for each output image; for single-output algorithms, only a single integer should be provided. If omitted, the command will use the lmax of the corresponding response function (i.e based on its number of coefficients), up to a maximum of 8.",
	"optional": true,
	"allow_multiple": false,
	"arguments": [
	{
	"id": "order",
	"description": "",
	"type": "int seq",
	"optional": false,
	"allow_multiple": false

This is another one that should be comma-separated. Unclear if it is.

[nx10]

Can we find any instances where it shouldn't be comma separated? If not we can remove that hacky check

[kaitj]

niwrap/extraction/mrtrix/json_docs/reference/commands/dirstat.json

Lines 51 to 61 in 50184d4

	"id": "output",
	"description": "output selected metrics as a space-delimited list, suitable for use in scripts. This will produce one line of values per selected shell. Valid metrics are as specified in the description above.",
	"optional": true,
	"allow_multiple": false,
	"arguments": [
	{
	"id": "list",
	"description": "",
	"type": "undefined",
	"optional": false,
	"allow_multiple": false

at least this one (from what i could find in a quick search)