From 681cfe2db7064b73d1421ffa705f6e04feb104bb Mon Sep 17 00:00:00 2001 From: Tristan Glatard Date: Mon, 24 Oct 2016 14:28:53 -0400 Subject: [PATCH] Minor updates --- cbrain_task_descriptors/qeeg.json | 106 +++++++++++++++--------------- 1 file changed, 53 insertions(+), 53 deletions(-) diff --git a/cbrain_task_descriptors/qeeg.json b/cbrain_task_descriptors/qeeg.json index 5eccdf7..8e4284e 100644 --- a/cbrain_task_descriptors/qeeg.json +++ b/cbrain_task_descriptors/qeeg.json @@ -2,7 +2,7 @@ "name": "qeeg", "tool-version": "undefined", "description": "qeeg application", - "command-line": "qeegt.sh [input_directory]/[basename] [state] [lwin] [fmin] [freqres] [fmax] [wbands] [brain] [pg_apply] [bbsm] [nbsm] [spectra] [bbsmz] [nbsmz] [ssz] [corr] [cohe] [phdiff] [fcorr] [storexyz]", + "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]", "docker-image": "mcin/qeeg:latest", "docker-index": "http://index.docker.io", "schema-version": "0.2", @@ -10,16 +10,15 @@ "id": "input_directory", "name": "Input directory", "type": "File", - "description": "Directory containing the files to process", + "description": "Directory containing the files to process.", "command-line-key": "[input_directory]", - "command-line-flag": "--input", "list": false, "optional": false }, { "id": "basename", "name": "Basename", "type": "String", - "description": "Basename of the file to process in the input directory", + "description": "Basename of the file to process in the input directory.", "command-line-key": "[basename]", "list": false, "optional": false @@ -27,8 +26,7 @@ "id": "state", "name": "State", "type": "String", - "command-line-flag": "--state", - "description": "Example: \"A\". EEG state to be analyzed. The program will look for existing analysis windows labelled as state 'A' (Eyes Closed)", + "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", "command-line-key": "[state]", "list": false, @@ -37,9 +35,8 @@ "id": "lwin", "name": "Window length", "type": "Number", - "command-line-flag": "--lwin", "default-value": 2.56, - "description": "Length of the analysis window in seconds", + "description": "Length of the analysis window in seconds.", "command-line-key": "[lwin]", "minimum": 0, "list": false, @@ -47,10 +44,9 @@ }, { "id": "fmin", "name": "fmin", - "command-line-flag": "--fmin", "default-value": 0.390625, "type": "Number", - "description": "Low cut frequency for analysis. Example: \"0.390625\"", + "description": "Low cut frequency for analysis. Example: \"0.390625\".", "command-line-key": "[fmin]", "minimum": 0, "list": false, @@ -59,147 +55,151 @@ "id": "freqres", "name": "freqres", "type": "Number", - "command-line-flag": "--freqres", "default-value": 0.390625, - "description": "Fequency 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", + "description": "Fequency 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.", "command-line-key": "[freqres]", "list": false, "optional": false }, { "id": "fmax", "name": "fmax", - "command-line-flag": "--fmax", "type": "Number", "default-value": 19.11, - "description": "High cut frequency for analysis. Example: \"19.11\"", + "description": "High cut frequency for analysis. Example: \"19.11\".", "command-line-key": "[fmax]", "list": false, "optional": false }, { "id": "wbands", "name": "wbands", - "command-line-flag": "--wbands", "default-value": "1.56 3.51; 3.9 7.41; 7.8 12.48; 12.87 19.11; 1.56 30", "type": "String", - "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 30\"", + "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 30\".", "command-line-key": "[wbands]", "list": false, "optional": false }, { "id": "brain", "name": "Brain", - "description": "Restricts the inverse solution to only gray matter. Otherwise, deep structure (basal ganglia) will be included in the grid", + "description": "Restricts the inverse solution to only gray matter. Otherwise, deep structure (basal ganglia) will be included in the grid.", "default-value": true, "type": "Flag", "command-line-key": "[brain]", - "command-line-flag": "--brain" + "command-line-flag": "--brain", + "optional": true }, { "id": "pg_apply", "name": "PG Apply", "default-value": true, - "type": "Number", - "description": "Substracts the Global Scale Factor (Geometric Power) from the EEG signal", + "type": "Flag", + "description": "Substracts the Global Scale Factor (Geometric Power) from the EEG signal.", "command-line-key": "[pg_apply]", - "command-line-flag": "--pg_apply" + "command-line-flag": "--pg_apply", + "optional": true }, { "id": "bbsm", "name": "Broad Band Spectral Model", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the Broad Band Spectral Model.", "command-line-key": "[bbsm]", - "command-line-flag": "--bbsm" + "command-line-flag": "--bbsm", + "optional": true }, { "id": "nbsm", "name": "Narrow Band Spectral Model", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the Narrow Band Spectral Model.", "command-line-key": "[nbsm]", - "command-line-flag": "--nbsm" + "command-line-flag": "--nbsm", + "optional": true }, { "id": "spectra", "name": "Spectra", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the Spectra at the EEG sources.", "command-line-key": "[spectra]", - "command-line-flag": "--spectra" + "command-line-flag": "--spectra", + "optional": true }, { "id": "bbsmz", "name": "Broad Band Spectral Model Z values", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the Broad Band Spectral Model Z values.", "command-line-key": "[bbsmz]", - "command-line-flag": "--bbsmz" + "command-line-flag": "--bbsmz", + "optional": true }, { "id": "nbsmz", "name": "Narrow Band Spectral Model Z values", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the Narrow Band Spectral Model Z values.", "command-line-key": "[nbsmz]", - "command-line-flag": "--nbsmz" + "command-line-flag": "--nbsmz", + "optional": true }, { - "id": "Source Spectra Z", - "name": "SSZ", + "id": "ssz", + "name": "Source Spectra Z", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the Sources Spectra Z values.", "command-line-key": "[ssz]", - "command-line-flag": "--ssz" + "command-line-flag": "--ssz", + "optional": true }, { "id": "corr", "name": "Correlations matrix", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the correlations matrix bewteen all pairs of channels for each epoch.", "command-line-key": "[corr]", - "command-line-flag": "--corr" + "command-line-flag": "--corr", + "optional": true }, { "id": "cohe", "name": "Coherence matrix", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the coherence matrix bewteen all pairs of channels for each frequency.", "command-line-key": "[cohe]", - "command-line-flag": "--cohe" + "command-line-flag": "--cohe", + "optional": true }, { "id": "phdiff", "name": "Phase difference matrix", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the phase difference matrix bewteen all pairs of channels for each frequency.", - "command-line-key": "[phdiff]", - "command-line-flag": "--phdiff" + "command-line-key": "[phdiff]", + "command-line-flag": "--phdiff", + "optional": true }, { "id": "fcorr", "name": "Frequency domain correlations", "type": "Flag", - "default-value": true + "default-value": true, "description": "Calculates the frequency domain correlations bewteen all pairs of channels for each frequency and each epoch.", "command-line-key": "[fcorr]", - "command-line-flag": "--fcorr" + "command-line-flag": "--fcorr", + "optional": true + }, { "id": "storexyz", "name": "XYZ components", "type": "Flag", - "default-value": true + "default-value": true, "description": "Stores the XYZ components of the solutions at the sources.", "command-line-key": "[storexyz]", - "command-line-flag": "--storezyx" + "command-line-flag": "--storexyz", + "optional": true } ], - "groups" : [ - { - "id" : "flags", - "name" : "Flags", - "members" : [ "bbsm", "nbsm", "spectra", "bbsmz", "nbsmz", "ssz", "corr", "cohe", "phdiff", "fcorr", "storexyz" ] - } - ], "output-files": [ { "id": "folder_out",