{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "filter_10xh5",
  "description": "Filter a 10x h5 dataset.\n",
  "type": "object",
  "$defs": {
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "An h5 file from the 10x genomics website.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"pbmc_1k_protein_v3_raw_feature_bc_matrix.h5\"`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output h5 file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5\"`, direction: `output`, example: `\"pbmc_1k_protein_v3_raw_feature_bc_matrix_filtered.h5\"`. ",
          "default": "$id.$key.output.h5"
        },
        "min_library_size": {
          "type": "integer",
          "description": "Minimum library size.",
          "help_text": "Type: `integer`, multiple: `False`, default: `0`. ",
          "default": 0
        },
        "min_cells_per_gene": {
          "type": "integer",
          "description": "Minimum number of cells per gene.",
          "help_text": "Type: `integer`, multiple: `False`, default: `0`. ",
          "default": 0
        },
        "keep_feature_types": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Specify which feature types will never be filtered out",
          "help_text": "Type: `string`, multiple: `True`, example: `[\"Antibody Capture\"]`. "
        },
        "verbose": {
          "type": "boolean",
          "description": "Increase verbosity",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        }
      }
    },
    "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": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
