{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "concatenate_h5mu",
  "description": "Concatenate observations from samples in several (uni- and/or multi-modal) MuData files into a single file.\n",
  "type": "object",
  "$defs": {
    "Dataset input": {
      "title": "Dataset input",
      "type": "object",
      "description": "Dataset input using nf-tower \"dataset\" or \"data explorer\". Allows for the input of multiple         parameter sets to initialise a Nextflow channel.",
      "properties": {
        "param_list": {
          "description": "Dataset input can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml                 blob. The names of the input fields (e.g. csv columns, json keys) need to be an exact match with the workflow input parameters.",
          "type": "string",
          "default": "",
          "format": "file-path",
          "mimetype": "text/csv"
        }
      }
    },
    "arguments": {
      "title": "Arguments",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "format": "path",
          "exists": true,
          "description": "Paths to the different samples to be concatenated.",
          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"sample_paths\"]`. "
        },
        "modality": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Only output concatenated objects for the provided modalities",
          "help_text": "Type: `string`, multiple: `True`. "
        },
        "input_id": {
          "type": "array",
          "items": {
            "type": "string"
          },
          "description": "Names of the different samples that have to be concatenated",
          "help_text": "Type: `string`, multiple: `True`. "
        },
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output location for the concatenated MuData object file.\n",
          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "obs_sample_name": {
          "type": "string",
          "description": "Name of the .obs key under which to add the sample names.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"sample_id\"`. ",
          "default": "sample_id"
        },
        "other_axis_mode": {
          "type": "string",
          "description": "How to handle the merging of other axis (var, obs, ...).\n\n  - None: keep no data\n  - same: only keep elements of the matrices which are the same in each of the samples\n  - unique: only keep elements for which there is only 1 possible value (1 value that can occur in multiple samples)\n  - first: keep the annotation from the first sample\n  - only: keep elements that show up in only one of the objects (1 unique element in only 1 sample)\n  - move: identical to 'same', but moving the conflicting values to .varm or .obsm\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"move\"`, choices: ``same`, `unique`, `first`, `only`, `concat`, `move``. ",
          "enum": [
            "same",
            "unique",
            "first",
            "only",
            "concat",
            "move"
          ],
          "default": "move"
        },
        "uns_merge_mode": {
          "type": "string",
          "description": "How to handle the merging of .uns across modalities\n  - None: keep no data\n  - same: only keep elements of the matrices which are the same in each of the samples\n  - unique: only keep elements for which there is only 1 possible value (1 value that can occur in multiple samples)\n  - first: keep the annotation from the first sample\n  - only: keep elements that show up in only one of the objects (1 unique element in only 1 sample)\n  - make_unique: identical to 'unique', but keys which are not unique are made unique by prefixing them with the sample id.\n",
          "help_text": "Type: `string`, multiple: `False`, default: `\"make_unique\"`, choices: ``same`, `unique`, `first`, `only`, `make_unique``. ",
          "enum": [
            "same",
            "unique",
            "first",
            "only",
            "make_unique"
          ],
          "default": "make_unique"
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata objects.\nBy default no compression is applied.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
          "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": "Path to an output directory.",
          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
        }
      }
    }
  },
  "allOf": [
    {
      "$ref": "#/$defs/arguments"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
