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Regenerate value-keys (upper-case id) (#185)
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* Refactor suspicious command line QC script

* Regenerate value keys (upper-case id)
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nx10 authored Nov 27, 2024
1 parent c1e8776 commit 88ded06
Showing 806 changed files with 4,885 additions and 4,876 deletions.
16 changes: 8 additions & 8 deletions descriptors/afni/1dBport.json
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
"name": "1dBport",
"author": "AFNI Developers",
"description": "Creates a set of columns of sines and cosines for bandpassing via regression.",
"command-line": "1dBport [BAND] [INVERT_FLAG] [NOZERO_FLAG] [QUAD_FLAG] [INPUT_DATASET] [INPUT_1D_FILE] [NODATA_OPTION] [TR_VALUE] [CONCAT_FILE]",
"command-line": "1dBport [BAND] [INVERT] [NOCONST] [QUAD] [INPUT_DATASET] [INPUT_1D_FILE] [NODATA] [TR] [CONCAT]",
"container-image": {
"type": "docker",
"image": "afni/afni_make_build:AFNI_24.2.06"
@@ -24,7 +24,7 @@
{
"command-line-flag": "-invert",
"description": "Invert the selection after computing which frequency indexes correspond to the input band(s).",
"value-key": "[INVERT_FLAG]",
"value-key": "[INVERT]",
"type": "Flag",
"optional": true,
"id": "invert",
@@ -33,7 +33,7 @@
{
"command-line-flag": "-nozero",
"description": "Do NOT generate the 0 frequency (constant) component when fbot = 0.",
"value-key": "[NOZERO_FLAG]",
"value-key": "[NOZERO]",
"type": "Flag",
"optional": true,
"id": "nozero",
@@ -42,7 +42,7 @@
{
"command-line-flag": "-noconst",
"description": "Same as -nozero. Do NOT generate the 0 frequency (constant) component when fbot = 0.",
"value-key": "[NOZERO_FLAG]",
"value-key": "[NOCONST]",
"type": "Flag",
"optional": true,
"id": "noconst",
@@ -51,7 +51,7 @@
{
"command-line-flag": "-quad",
"description": "Add regressors for linear and quadratic trends.",
"value-key": "[QUAD_FLAG]",
"value-key": "[QUAD]",
"type": "Flag",
"optional": true,
"id": "quad",
@@ -78,7 +78,7 @@
{
"command-line-flag": "-nodata",
"description": "Specify the number of time points and optionally TR value for the simulation.",
"value-key": "[NODATA_OPTION]",
"value-key": "[NODATA]",
"type": "Number",
"list": true,
"min-list-entries": 1,
@@ -90,7 +90,7 @@
{
"command-line-flag": "-TR",
"description": "Set the time step duration.",
"value-key": "[TR_VALUE]",
"value-key": "[TR]",
"type": "Number",
"optional": true,
"id": "tr",
@@ -99,7 +99,7 @@
{
"command-line-flag": "-concat",
"description": "Specify the list of start indexes for concatenated runs.",
"value-key": "[CONCAT_FILE]",
"value-key": "[CONCAT]",
"type": "File",
"optional": true,
"id": "concat",
18 changes: 9 additions & 9 deletions descriptors/afni/1dCorrelate.json
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
"name": "1dCorrelate",
"author": "AFNI Developers",
"description": "1dCorrelate calculates the correlation coefficients between columns of input 1D files along with confidence intervals via a bootstrap procedure.",
"command-line": "1dCorrelate [METHOD] [BOOTSTRAP_REPLICATES] [CONFIDENCE_INTERVAL] [BLOCK_RESAMPLING] [INPUT_FILES]",
"command-line": "1dCorrelate [KTAUB] [NBOOT] [ALPHA] [BLK] [INPUT_FILES]",
"inputs": [
{
"description": "Input 1D files",
@@ -17,7 +17,7 @@
{
"command-line-flag": "-Pearson",
"description": "Pearson correlation (the default method)",
"value-key": "[METHOD]",
"value-key": "[PEARSON]",
"type": "Flag",
"optional": true,
"id": "pearson",
@@ -26,7 +26,7 @@
{
"command-line-flag": "-Spearman",
"description": "Spearman (rank) correlation (more robust versus outliers)",
"value-key": "[METHOD]",
"value-key": "[SPEARMAN]",
"type": "Flag",
"optional": true,
"id": "spearman",
@@ -35,7 +35,7 @@
{
"command-line-flag": "-Quadrant",
"description": "Quadrant (binarized) correlation (most robust, but weaker)",
"value-key": "[METHOD]",
"value-key": "[QUADRANT]",
"type": "Flag",
"optional": true,
"id": "quadrant",
@@ -44,7 +44,7 @@
{
"command-line-flag": "-Ktaub",
"description": "Kendall's tau_b correlation (popular somewhere, maybe)",
"value-key": "[METHOD]",
"value-key": "[KTAUB]",
"type": "Flag",
"optional": true,
"id": "ktaub",
@@ -53,7 +53,7 @@
{
"command-line-flag": "-nboot",
"description": "Set the number of bootstrap replicates",
"value-key": "[BOOTSTRAP_REPLICATES]",
"value-key": "[NBOOT]",
"type": "Number",
"optional": true,
"id": "nboot",
@@ -62,7 +62,7 @@
{
"command-line-flag": "-alpha",
"description": "Set the 2-sided confidence interval width to '100-A' percent.",
"value-key": "[CONFIDENCE_INTERVAL]",
"value-key": "[ALPHA]",
"type": "Number",
"minimum": 1,
"maximum": 20,
@@ -73,7 +73,7 @@
{
"command-line-flag": "-block",
"description": "Use variable-length block resampling to account for serial correlation",
"value-key": "[BLOCK_RESAMPLING]",
"value-key": "[BLOCK]",
"type": "Flag",
"optional": true,
"id": "block",
@@ -82,7 +82,7 @@
{
"command-line-flag": "-blk",
"description": "Alternate flag for variable-length block resampling",
"value-key": "[BLOCK_RESAMPLING]",
"value-key": "[BLK]",
"type": "Flag",
"optional": true,
"id": "blk",
8 changes: 4 additions & 4 deletions descriptors/afni/1dMarry.json
Original file line number Diff line number Diff line change
@@ -5,15 +5,15 @@
"descriptor-url": "https://github.com/afni/afni/blob/master/src/1dMarry.c",
"description": "Joins together 2 (or more) ragged-right .1D files, for use with 3dDeconvolve -stim_times_AM2, or breaks up 1 married file into 2 (or more) single-valued files.",
"url": "https://afni.nimh.nih.gov/",
"command-line": "1dMarry [SEPARATORS] [DIVORCE_FLAG] [FILE1] [FILE2]",
"command-line": "1dMarry [SEP] [DIVORCE] [FILES] [FILE2]",
"container-image": {
"type": "docker",
"image": "afni/afni_make_build:AFNI_24.2.06"
},
"inputs": [
{
"description": "Input file(s) to be married or divorced.",
"value-key": "[FILE1]",
"value-key": "[FILES]",
"type": "File",
"list": true,
"optional": false,
@@ -23,7 +23,7 @@
{
"command-line-flag": "-sep",
"description": "Separator(s) for marrying files. The first character is used as the separator between values 1 and 2, the second character between values 2 and 3, etc.",
"value-key": "[SEPARATORS]",
"value-key": "[SEP]",
"type": "String",
"optional": true,
"id": "sep",
@@ -32,7 +32,7 @@
{
"command-line-flag": "-divorce",
"description": "Divorce mode: splits married file into separate files.",
"value-key": "[DIVORCE_FLAG]",
"value-key": "[DIVORCE]",
"type": "Flag",
"optional": true,
"id": "divorce",
6 changes: 3 additions & 3 deletions descriptors/afni/1dNLfit.json
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
"name": "1dNLfit",
"author": "AFNI Developers",
"description": "Program to fit a model to a vector of data. The model is given by a symbolic expression, with parameters to be estimated.",
"command-line": "1dNLfit [EXPRESSION] [INDEPENDENT_VAR] [PARAMETERS] [DEPENDENT_DATA] [METHOD_FLAG]",
"command-line": "1dNLfit [EXPRESSION] [INDEPENDENT_VARIABLE] [PARAMETERS] [DEPENDENT_DATA] [METHOD]",
"inputs": [
{
"command-line-flag": "-expr",
@@ -17,7 +17,7 @@
{
"command-line-flag": "-indvar",
"description": "Indicates which variable in '-expr' is the independent variable. All other symbols are parameters, which are either fixed (constants) or variables to be estimated. Read the values of the independent variable from 1D file.",
"value-key": "[INDEPENDENT_VAR]",
"value-key": "[INDEPENDENT_VARIABLE]",
"type": "String",
"optional": false,
"id": "independent_variable",
@@ -45,7 +45,7 @@
{
"command-line-flag": "-meth",
"description": "Set the method for fitting: '1' for L1, '2' for L2 (default is L2).",
"value-key": "[METHOD_FLAG]",
"value-key": "[METHOD]",
"type": "Number",
"integer": true,
"optional": true,
12 changes: 6 additions & 6 deletions descriptors/afni/1dRplot.json
Original file line number Diff line number Diff line change
@@ -3,15 +3,15 @@
"name": "1dRplot",
"author": "AFNI Developers",
"description": "Program for plotting a 1D file",
"command-line": "1dRplot [INPUT] [OPTIONS]",
"command-line": "1dRplot [INPUT_FILE] [OPTIONS]",
"container-image": {
"type": "docker",
"image": "afni/afni_make_build:AFNI_24.2.06"
},
"inputs": [
{
"description": "Input 1D file to plot",
"value-key": "[INPUT]",
"value-key": "[INPUT_FILE]",
"command-line-flag": "-input",
"type": "File",
"optional": false,
@@ -20,7 +20,7 @@
},
{
"description": "Output prefix. See also -save.",
"value-key": "[PREFIX]",
"value-key": "[OUTPUT_PREFIX]",
"command-line-flag": "-prefix",
"type": "String",
"optional": true,
@@ -78,7 +78,7 @@
},
{
"description": "Text to be placed at left Y margin. You need one string per column.",
"value-key": "[LEFT_Y_TEXT]",
"value-key": "[LEFT_Y_MARGIN_TEXT]",
"command-line-flag": "-col.text.lym",
"type": "String",
"optional": true,
@@ -87,7 +87,7 @@
},
{
"description": "Text to be placed at right Y margin. You need one string per column.",
"value-key": "[RIGHT_Y_TEXT]",
"value-key": "[RIGHT_Y_MARGIN_TEXT]",
"command-line-flag": "-col.text.rym",
"type": "String",
"optional": true,
@@ -183,7 +183,7 @@
},
{
"description": "Save plot and quit. No need for -prefix with this option.",
"value-key": "[SAVE]",
"value-key": "[SAVE_PLOT]",
"command-line-flag": "-save",
"type": "Flag",
"optional": true,
10 changes: 5 additions & 5 deletions descriptors/afni/1dSEM.json
Original file line number Diff line number Diff line change
@@ -5,15 +5,15 @@
"descriptor-url": "https://afni.nimh.nih.gov/sscc/gangc/PathAna.html",
"description": "Computes path coefficients for connection matrix in Structural Equation Modeling (SEM).",
"url": "https://afni.nimh.nih.gov/",
"command-line": "1dSEM [THETA_FILE] [CORRELATION_MATRIX] [RESIDUAL_VARIANCE] [DEGREES_OF_FREEDOM] [OPTIONS]",
"command-line": "1dSEM [THETA] [CORRELATION_MATRIX] [RESIDUAL_VARIANCE] [DEGREES_OF_FREEDOM] [OPTIONS]",
"container-image": {
"type": "docker",
"image": "afni/afni_make_build:AFNI_24.2.06"
},
"inputs": [
{
"description": "Connection matrix 1D file with initial representation",
"value-key": "[THETA_FILE]",
"value-key": "[THETA]",
"type": "File",
"optional": false,
"id": "theta",
@@ -50,7 +50,7 @@
{
"command-line-flag": "-max_iter",
"description": "Maximum number of iterations for convergence (Default=10000). Values can range from 1 to any positive integer less than 10000.",
"value-key": "[MAX_ITER]",
"value-key": "[MAX_ITERATIONS]",
"type": "Number",
"integer": true,
"optional": true,
@@ -60,7 +60,7 @@
{
"command-line-flag": "-nrand",
"description": "Number of random trials before optimization (Default = 100).",
"value-key": "[NRAND]",
"value-key": "[NUMBER_RANDOM_TRIALS]",
"type": "Number",
"integer": true,
"optional": true,
@@ -82,7 +82,7 @@
{
"command-line-flag": "-calccost",
"description": "No modeling at all, just calculate the cost function for the coefficients as given in the theta file.",
"value-key": "[CALC_COST]",
"value-key": "[CALCULATE_COST]",
"type": "Flag",
"optional": true,
"id": "calculate_cost",
12 changes: 6 additions & 6 deletions descriptors/afni/1dTsort.json
Original file line number Diff line number Diff line change
@@ -5,11 +5,11 @@
"descriptor-url": "https://github.com/afni/afni",
"description": "Sorts each column of the input 1D file and writes result to stdout.",
"url": "https://afni.nimh.nih.gov/",
"command-line": "1dTsort [ORDER_OPTION] [TRANSPOSE_FLAG] [COLUMN] [IMODE_FLAG] [INPUT_FILE]",
"command-line": "1dTsort [DEC_ORDER] [TRANSPOSE] [COLUMN] [IMODE] [INFILE]",
"inputs": [
{
"description": "Input 1D file to be sorted.",
"value-key": "[INPUT_FILE]",
"value-key": "[INFILE]",
"type": "File",
"optional": false,
"id": "infile",
@@ -18,7 +18,7 @@
{
"command-line-flag": "-inc",
"description": "Sort into increasing order [default]",
"value-key": "[ORDER_OPTION]",
"value-key": "[INC_ORDER]",
"type": "Flag",
"optional": true,
"id": "inc_order",
@@ -27,7 +27,7 @@
{
"command-line-flag": "-dec",
"description": "Sort into decreasing order",
"value-key": "[ORDER_OPTION]",
"value-key": "[DEC_ORDER]",
"type": "Flag",
"optional": true,
"id": "dec_order",
@@ -36,7 +36,7 @@
{
"command-line-flag": "-flip",
"description": "Transpose the file before output.",
"value-key": "[TRANSPOSE_FLAG]",
"value-key": "[TRANSPOSE]",
"type": "Flag",
"optional": true,
"id": "transpose",
@@ -54,7 +54,7 @@
{
"command-line-flag": "-imode",
"description": "Typecast all values to integers, return the mode in the input then exit. No sorting results are returned.",
"value-key": "[IMODE_FLAG]",
"value-key": "[IMODE]",
"type": "Flag",
"optional": true,
"id": "imode",
4 changes: 2 additions & 2 deletions descriptors/afni/1dUpsample.json
Original file line number Diff line number Diff line change
@@ -3,7 +3,7 @@
"name": "1dUpsample",
"author": "AFNI Developers",
"description": "Upsamples a 1D time series to a finer time grid.",
"command-line": "1dUpsample [UPSAMPLE_FACTOR] [INPUT_FILE] [INTERPOLATION]",
"command-line": "1dUpsample [UPSAMPLE_FACTOR] [INPUT_FILE] [LINEAR_INTERPOLATION]",
"inputs": [
{
"description": "Upsample factor (integer from 2..32)",
@@ -26,7 +26,7 @@
{
"command-line-flag": "-one",
"description": "Use 1st order polynomials (i.e., linear interpolation) instead of 7th order polynomials",
"value-key": "[INTERPOLATION]",
"value-key": "[LINEAR_INTERPOLATION]",
"type": "Flag",
"optional": true,
"id": "linear_interpolation",
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