CI
cd0af18851
Build pipeline: vsh-ci-dev-k8tz4
Source commit: 2dbe3b7231
Source message: Fix pointers to test resources
146 lines
5.8 KiB
JSON
146 lines
5.8 KiB
JSON
{
|
|
"$schema": "http://json-schema.org/draft-07/schema",
|
|
"title": "scale",
|
|
"description": "Scale data to unit variance and zero mean.\n",
|
|
"type": "object",
|
|
"definitions": {
|
|
|
|
|
|
|
|
"arguments" : {
|
|
"title": "Arguments",
|
|
"type": "object",
|
|
"description": "No description",
|
|
"properties": {
|
|
|
|
|
|
"input": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, required, example: `input.h5mu`. Input h5mu file",
|
|
"help_text": "Type: `file`, required, example: `input.h5mu`. Input h5mu file."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"modality": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, default: `rna`. List of modalities to process",
|
|
"help_text": "Type: `string`, default: `rna`. List of modalities to process."
|
|
,
|
|
"default": "rna"
|
|
}
|
|
|
|
|
|
,
|
|
"input_layer": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Input layer with data to scale",
|
|
"help_text": "Type: `string`. Input layer with data to scale. Uses .X by default"
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"output_layer": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`. Output layer where scaled data will be stored",
|
|
"help_text": "Type: `string`. Output layer where scaled data will be stored. If not specified, .X will be used."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"max_value": {
|
|
"type":
|
|
"number",
|
|
"description": "Type: `double`. Clip (truncate) to this value after scaling",
|
|
"help_text": "Type: `double`. Clip (truncate) to this value after scaling. Does not clip by default."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"zero_center": {
|
|
"type":
|
|
"boolean",
|
|
"description": "Type: `boolean_false`, default: `true`. If set, omit zero-centering variables, which allows to handle sparse input efficiently",
|
|
"help_text": "Type: `boolean_false`, default: `true`. If set, omit zero-centering variables, which allows to handle sparse input efficiently."
|
|
,
|
|
"default": "True"
|
|
}
|
|
|
|
|
|
,
|
|
"output": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `file`, required, default: `$id.$key.output.h5mu`. Output h5mu file",
|
|
"help_text": "Type: `file`, required, default: `$id.$key.output.h5mu`. Output h5mu file."
|
|
,
|
|
"default": "$id.$key.output.h5mu"
|
|
}
|
|
|
|
|
|
,
|
|
"output_compression": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. The compression format to be used on the output h5mu object",
|
|
"help_text": "Type: `string`, example: `gzip`, choices: ``gzip`, `lzf``. The compression format to be used on the output h5mu object.",
|
|
"enum": ["gzip", "lzf"]
|
|
|
|
|
|
}
|
|
|
|
|
|
}
|
|
},
|
|
|
|
|
|
"nextflow input-output arguments" : {
|
|
"title": "Nextflow input-output arguments",
|
|
"type": "object",
|
|
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
|
|
"properties": {
|
|
|
|
|
|
"publish_dir": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
|
|
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
|
|
|
|
}
|
|
|
|
|
|
,
|
|
"param_list": {
|
|
"type":
|
|
"string",
|
|
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
|
|
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
|
|
"hidden": true
|
|
|
|
}
|
|
|
|
|
|
}
|
|
}
|
|
},
|
|
"allOf": [
|
|
|
|
{
|
|
"$ref": "#/definitions/arguments"
|
|
},
|
|
|
|
{
|
|
"$ref": "#/definitions/nextflow input-output arguments"
|
|
}
|
|
]
|
|
}
|