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correct verbiage, add a version of eegt with automatic CBRAIN type assignment for output #2

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correct verbiage, add a version of eegt with automatic CBRAIN type assignment for output #2

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cd595f3
verbiage - correct few typos
MontrealSergiy Oct 10, 2025
080c500
add version with result type assignment #20
MontrealSergiy Oct 10, 2025
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272 changes: 272 additions & 0 deletions boutiques_descriptors/qeegt.json
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{
"tool-version": "undefined",
"name": "qEEGt",
"author": "Neuroinformatics Collaboratory",
"descriptor-url": "https://github.com/big-data-lab-team/cbrain-plugins-eeg/blob/master/cbrain_task_descriptors/qeeg.json",
"command-line": "qeegt.sh --input [input_directory]/[basename] --state [state] --lwin [lwin] --fmin [fmin] --freqres [freqres] --fmax [fmax] --wbands [wbands] [brain] [pg_apply] [bbsm] [nbsm] [spectra] [bbsmz] [nbsmz] [ssz] [corr] [cohe] [phdiff] [fcorr] [storexyz] [OUTPUT]",
"command-line": "qeegt.sh --input [input_directory]/[basename] --state [state] --lwin [lwin] --fmin [fmin] --freqres [freqres] --fmax [fmax] --wbands [wbands] [brain] [pg_apply] [bbsm] [nbsm] [spectra] [bbsmz] [nbsmz] [ssz] [corr] [cohe] [phdiff] [fcorr] [storexyz] [OUTPUT] ",
"online-platform-urls": [
"https://portal.cbrain.mcgill.ca"
],
"inputs": [
{
"description": "Directory containing the files to process.",
"value-key": "[input_directory]",
"optional": false,
"list": false,
"type": "File",
"id": "input_directory",
"name": "Input directory"
},
{
"description": "Basename of the file to process in the input directory.",
"value-key": "[basename]",
"optional": false,
"list": false,
"type": "String",
"id": "basename",
"name": "Basename"
},
{
"description": "Example: \"A\". EEG state to be analyzed. The program will look for existing analysis windows labelled as state 'A' (Eyes Closed).",
"default-value": "A",
"value-key": "[state]",
"optional": false,
"list": false,
"type": "String",
"id": "state",
"name": "State"
},
{
"description": "Length of the analysis window in seconds.",
"default-value": 2.56,
"value-key": "[lwin]",
"optional": false,
"list": false,
"minimum": 0,
"type": "Number",
"id": "lwin",
"name": "Window length"
},
{
"description": "Low cut frequency for analysis. Example: \"0.390625\".",
"default-value": 0.390625,
"value-key": "[fmin]",
"optional": false,
"list": false,
"minimum": 0,
"type": "Number",
"id": "fmin",
"name": "fmin"
},
{
"description": "Frequency resolution for analysis. Example: \"0.390625\". The analysis will use a frequency band like this: fmin:freqres:fmax. The program will compare this interval with the interval that is obtained for the real frequency parameters of the signal and will match both of them.",
"default-value": 0.390625,
"value-key": "[freqres]",
"optional": false,
"list": false,
"type": "Number",
"id": "freqres",
"name": "freqres"
},
{
"description": "High cut frequency for analysis. Example: \"19.11\".",
"default-value": 19.11,
"value-key": "[fmax]",
"optional": false,
"list": false,
"type": "Number",
"id": "fmax",
"name": "fmax"
},
{
"description": "Broad Bands definition. A string representing a 5x2 matrix of real numbers, where rows are separated by ';' and columns by spaces. Example: \"1.56 3.51; 3.9 7.41; 7.8 12.48; 12.87 19.11; 1.56 19.11\".",
"default-value": "1.56 3.51; 3.9 7.41; 7.8 12.48; 12.87 19.11; 1.56 19.11",
"value-key": "[wbands]",
"optional": false,
"list": false,
"type": "String",
"id": "wbands",
"name": "wbands"
},
{
"command-line-flag": "--brain",
"description": "Restricts the inverse solution to only gray matter. Otherwise, deep structure (basal ganglia) will be included in the grid.",
"default-value": true,
"value-key": "[brain]",
"optional": true,
"type": "Flag",
"id": "brain",
"name": "Brain"
},
{
"command-line-flag": "--pg_apply",
"description": "Subtracts the Global Scale Factor (Geometric Power) from the EEG signal.",
"default-value": true,
"value-key": "[pg_apply]",
"optional": true,
"type": "Flag",
"id": "pg_apply",
"name": "PG Apply"
},
{
"command-line-flag": "--bbsm",
"description": "Calculates the Broad Band Spectral Model.",
"default-value": true,
"value-key": "[bbsm]",
"optional": true,
"type": "Flag",
"id": "bbsm",
"name": "Broad Band Spectral Model"
},
{
"command-line-flag": "--nbsm",
"description": "Calculates the Narrow Band Spectral Model.",
"default-value": true,
"value-key": "[nbsm]",
"optional": true,
"type": "Flag",
"id": "nbsm",
"name": "Narrow Band Spectral Model"
},
{
"command-line-flag": "--spectra",
"description": "Calculates the Spectra at the EEG sources.",
"default-value": true,
"value-key": "[spectra]",
"optional": true,
"type": "Flag",
"id": "spectra",
"name": "Spectra"
},
{
"command-line-flag": "--bbsmz",
"description": "Calculates the Broad Band Spectral Model Z values.",
"default-value": true,
"value-key": "[bbsmz]",
"optional": true,
"type": "Flag",
"id": "bbsmz",
"name": "Broad Band Spectral Model Z values"
},
{
"command-line-flag": "--nbsmz",
"description": "Calculates the Narrow Band Spectral Model Z values.",
"default-value": true,
"value-key": "[nbsmz]",
"optional": true,
"type": "Flag",
"id": "nbsmz",
"name": "Narrow Band Spectral Model Z values"
},
{
"command-line-flag": "--ssz",
"description": "Calculates the Sources Spectra Z values.",
"default-value": true,
"value-key": "[ssz]",
"optional": true,
"type": "Flag",
"id": "ssz",
"name": "Source Spectra Z"
},
{
"command-line-flag": "--corr",
"description": "Calculates the correlations matrix bewteen all pairs of channels for each epoch.",
"default-value": true,
"value-key": "[corr]",
"optional": true,
"type": "Flag",
"id": "corr",
"name": "Correlations matrix"
},
{
"command-line-flag": "--cohe",
"description": "Calculates the coherence matrix between all pairs of channels for each frequency.",
"default-value": true,
"value-key": "[cohe]",
"optional": true,
"type": "Flag",
"id": "cohe",
"name": "Coherence matrix"
},
{
"command-line-flag": "--phdiff",
"description": "Calculates the phase difference matrix between all pairs of channels for each frequency.",
"default-value": true,
"value-key": "[phdiff]",
"optional": true,
"type": "Flag",
"id": "phdiff",
"name": "Phase difference matrix"
},
{
"command-line-flag": "--fcorr",
"description": "Calculates the frequency domain correlations between all pairs of channels for each frequency and each epoch.",
"default-value": true,
"value-key": "[fcorr]",
"optional": true,
"type": "Flag",
"id": "fcorr",
"name": "Frequency domain correlations"
},
{
"command-line-flag": "--storexyz",
"description": "Stores the XYZ components of the solutions at the sources.",
"default-value": true,
"value-key": "[storexyz]",
"optional": true,
"type": "Flag",
"id": "storexyz",
"name": "XYZ components"
},
{
"id": "output",
"name": "Output Directory",
"type": "String",
"value-key": "[OUTPUT]",
"description": "Place to store outputs",
"command-line-flag": "--output",
"default-value": "results",
"optional": true
}
],
"container-image": {
"image": "mcin/qeeg:latest",
"type": "docker"
},
"schema-version": "0.5",
"output-files": [
{
"description": "A folder containing the output files and a copy of the input files.",
"list": false,
"id": "folder_out",
"optional": false,
"path-template": "[OUTPUT]",
"name": "Output folder"
}
],
"description": "qeeg application",
"tags": {
"domain": [
"neuroinformatics",
"eeg"
]
},
"custom": {
"cbrain:integrator_modules": {
"BoutiquesOutputFileTypeSetter": {
"folder_out": "ModCollection"
},
"BoutiquesInputRegexChecker": {
"basename": [
"[^;|`$&><\\\\]*",
"cannot contain special characters such as ;, |, `, <, >, $, &, \\"
]
},
"BoutiquesFileNameVerifier": [
"folder_out"
]
},
"cbrain:readonly-input-files": true
}
}
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