{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "prot_multisample",
  "description": "Processing unimodal multi-sample ADT data.",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "id": {
          "type": "string",
          "description": "ID of the concatenated file",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"concatenated\"`. "
        },
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to the samples.",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"dataset.h5mu\"`. "
        },
        "layer": {
          "type": "string",
          "description": "Input layer to use",
          "help_text": "Type: `string`, multiple: `False`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Destination path to the output.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        }
      }
    },
    "qc metrics calculation options": {
      "title": "QC metrics calculation options",
      "type": "object",
      "description": "No description",
      "properties": {
        "var_qc_metrics": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Keys to select a boolean (containing only True or False) column from .var.\nFor each cell, calculate the proportion of total values for genes which are labeled 'True', \ncompared to the total sum of the values for all genes",
          "help_text": "Type: `string`, multiple: `True`, example: `[\"ercc,highly_variable\"]`. "
        },
        "top_n_vars": {
          "type": "array",
          "items": {
            "type": "integer"
          },
          "description": "Number of top vars to be used to calculate cumulative proportions.\nIf not specified, proportions are not calculated",
          "help_text": "Type: `integer`, multiple: `True`, default: `[50,100,200,500]`. ",
          "default": [
            50,
            100,
            200,
            500
          ]
        },
        "output_obs_num_nonzero_vars": {
          "type": "string",
          "description": "Name of column in .obs describing, for each observation, the number of stored values\n(including explicit zeroes)",
          "help_text": "Type: `string`, multiple: `False`, default: `\"num_nonzero_vars\"`. ",
          "default": "num_nonzero_vars"
        },
        "output_obs_total_counts_vars": {
          "type": "string",
          "description": "Name of the column for .obs describing, for each observation (row),\nthe sum of the stored values in the columns.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"total_counts\"`. ",
          "default": "total_counts"
        },
        "output_var_num_nonzero_obs": {
          "type": "string",
          "description": "Name of column describing, for each feature, the number of stored values\n(including explicit zeroes)",
          "help_text": "Type: `string`, multiple: `False`, default: `\"num_nonzero_obs\"`. ",
          "default": "num_nonzero_obs"
        },
        "output_var_total_counts_obs": {
          "type": "string",
          "description": "Name of the column in .var describing, for each feature (column),\nthe sum of the stored values in the rows.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"total_counts\"`. ",
          "default": "total_counts"
        },
        "output_var_obs_mean": {
          "type": "string",
          "description": "Name of the column in .obs providing the mean of the values in each row.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"obs_mean\"`. ",
          "default": "obs_mean"
        },
        "output_var_pct_dropout": {
          "type": "string",
          "description": "Name of the column in .obs providing for each feature the percentage of\nobservations the feature does not appear on (i.e",
          "help_text": "Type: `string`, multiple: `False`, default: `\"pct_dropout\"`. ",
          "default": "pct_dropout"
        }
      }
    },
    "clr arguments": {
      "title": "CLR arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "clr_axis": {
          "type": "integer",
          "description": "Axis across which CLR is performed.",
          "help_text": "Type: `integer`, multiple: `False`, default: `0`. ",
          "default": 0
        }
      }
    },
    "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/inputs"
    },
    {
      "$ref": "#/$defs/outputs"
    },
    {
      "$ref": "#/$defs/qc metrics calculation options"
    },
    {
      "$ref": "#/$defs/clr arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
