{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "title": "lsi",
  "description": "Runs Latent Semantic Indexing. Computes cell embeddings, feature loadings and singular values. Uses the implementation of scipy.\n",
  "type": "object",
  "$defs": {
    "inputs": {
      "title": "Inputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "input": {
          "type": "string",
          "format": "path",
          "exists": true,
          "description": "Path to input h5mu file",
          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"input.h5mu\"`. "
        },
        "modality": {
          "type": "string",
          "description": "On which modality to run LSI on.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"atac\"`. ",
          "default": "atac"
        },
        "layer": {
          "type": "string",
          "description": "Use specified layer for expression values",
          "help_text": "Type: `string`, multiple: `False`. "
        },
        "var_input": {
          "type": "string",
          "description": "Column name in .var matrix that will be used to select which genes to run the LSI on",
          "help_text": "Type: `string`, multiple: `False`. "
        }
      }
    },
    "outputs": {
      "title": "Outputs",
      "type": "object",
      "description": "No description",
      "properties": {
        "output": {
          "type": "string",
          "format": "path",
          "description": "Output h5mu file.",
          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output.h5mu\"`, direction: `output`, example: `\"output.h5mu\"`. ",
          "default": "$id.$key.output.h5mu"
        },
        "obsm_output": {
          "type": "string",
          "description": "In which .obsm slot to store the resulting embedding.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"X_lsi\"`. ",
          "default": "X_lsi"
        },
        "varm_output": {
          "type": "string",
          "description": "In which .varm slot to store the resulting loadings matrix.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"lsi\"`. ",
          "default": "lsi"
        },
        "uns_output": {
          "type": "string",
          "description": "In which .uns slot to store the stdev.",
          "help_text": "Type: `string`, multiple: `False`, default: `\"lsi\"`. ",
          "default": "lsi"
        },
        "overwrite": {
          "type": "boolean",
          "description": "Allow overwriting .obsm, .varm and .uns slots.",
          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
          "default": false
        },
        "output_compression": {
          "type": "string",
          "description": "Compression format to use for the output AnnData and/or Mudata H5 files.\nBy default no compression is applied.\n",
          "help_text": "Type: `string`, multiple: `False`, example: `\"gzip\"`, choices: ``gzip`, `lzf``. ",
          "enum": [
            "gzip",
            "lzf"
          ]
        }
      }
    },
    "lsi options": {
      "title": "LSI options",
      "type": "object",
      "description": "No description",
      "properties": {
        "num_components": {
          "type": "integer",
          "description": "Number of components to compute.",
          "help_text": "Type: `integer`, multiple: `False`, default: `50`. ",
          "default": 50
        },
        "scale_embeddings": {
          "type": "boolean",
          "description": "Scale embeddings to zero mean and unit variance.",
          "help_text": "Type: `boolean`, multiple: `False`, default: `true`. ",
          "default": true
        }
      }
    },
    "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/lsi options"
    },
    {
      "$ref": "#/$defs/nextflow input-output arguments"
    }
  ]
}
