MSA.json

{
  "id": "MSA",
  "script": "App-MSA",
  "label": "Multiple sequence alignment variation service",
  "description": "Compute the multiple sequence alignment and analyze SNP/variance.",
  "parameters": [
    {
      "id": "input_status",
      "allow_multiple": false,
      "label": "The input status.",
      "required": 0,
      "default": "",
      "desc": "Indicates whether the input is already aligned.",
      "type": "enum",
      "enum": [
        "unaligned",
        "aligned"
      ]
    },
    {
      "id": "input_type",
      "allow_multiple": false,
      "label": "The type of input selected.",
      "required": 0,
      "default": "",
      "desc": "Selects a type of input file or data to be given to an aligner.",
      "type": "enum",
      "enum": [
        "input_group",
        "input_fasta",
        "input_sequence",
        "input_genomegroup",
        "input_featurelist",
        "input_genomelist"
      ]
    },
    {
      "id": "fasta_files",
      "type": "group",
      "allow_multiple": true,
      "required": 0,
      "default": null,
      "group": [
        {
          "id": "file",
          "required": 1,
          "label": "Fasta file",
          "desc": "homologous sequences",
          "wstype": "feature_protein_fasta",
          "type": "wstype"
        },
        {
          "id": "type",
          "label": "file format",
          "required": 1,
          "default": "feature_dna_fasta",
          "desc": "The file format type.",
          "type": "enum",
          "enum": [
            "feature_dna_fasta",
            "feature_protein_fasta"
          ]
        }
      ]
    },
    {
      "id": "select_genomegroup",
      "allow_multiple": true,
      "required": 0,
      "default": null,
      "label": "Genome groups",
      "desc": "Genome groups",
      "wstype": "genome_group",
      "type": "wstype"
    },
    {
      "id": "feature_groups",
      "allow_multiple": true,
      "required": 0,
      "default": null,
      "label": "Feature groups",
      "desc": "Feature groups",
      "wstype": "feature_group",
      "type": "wstype"
    },
    {
        "id": "feature_list",
        "allow_multiple": true,
        "required": 0,
        "default": null,
        "label": "feature list",
        "desc": "Feature List",
        "type": "string"
    },
    {
        "id": "genome_list",
        "allow_multiple": true,
        "required": 0,
        "default": null,
        "label": "genome list",
        "desc": "Genome List",
        "type": "string"
    },
    {
      "id": "aligner",
      "allow_multiple": false,
      "label": "multiple sequence aligner",
      "required": 0,
      "default": "Muscle",
      "desc": "Tool used for aligning multiple sequences to each other.",
      "type": "enum",
      "enum": [
        "Muscle",
        "Mafft",
        "progressiveMauve"
      ]
    },
    {
      "id": "alphabet",
      "allow_multiple": false,
      "label": "sequence alphabet",
      "required": 1,
      "default": "dna",
      "desc": "Determines which sequence alphabet is present.",
      "type": "enum",
      "enum": [
        "dna",
        "protein"
      ]
    },
    {
      "id": "fasta_keyboard_input",
      "allow_multiple": false,
      "desc": "Text input for a fasta file.",
      "required": 0,
      "default": "",
      "label": "fasta keyboard input",
      "type": "string"
    },
    {
      "id": "ref_type",
      "allow_multiple": false,
      "label": "Reference sequence type",
      "required": 0,
      "default": "none",
      "desc": "Selects the kind of reference sequence to be used.",
      "type": "enum",
      "enum": [
        "none",
        "string",
        "feature_id",
        "genome_id",
        "first"
      ]
    },
    {
      "id": "strategy",
      "allow_multiple": false,
      "desc": "Mafft alignment strategy method",
      "required": 0,
      "default": "auto",
      "enum": [
        "auto",
        "fftns1",
        "fftns2",
        "fftnsi",
        "einsi",
        "linsi",
        "ginsi"
      ]
    },
    {
      "id": "ref_string",
      "allow_multiple": false,
      "desc": "The identity of a reference sequence. It can be empty (no sequence), a string representing a sequence, or an id to download a sequence.",
      "required": 0,
      "default": "",
      "label": "reference sequence identity",
      "type": "string"
    },
    {
      "id": "output_path",
      "allow_multiple": false,
      "label": "Output Folder",
      "required": 1,
      "default": null,
      "desc": "Path to which the output will be written. Defaults to the directory containing the input data. ",
      "type": "folder"
    },
    {
      "id": "output_file",
      "allow_multiple": false,
      "label": "File Basename",
      "required": 1,
      "default": null,
      "desc": "Basename for the generated output files. Defaults to the basename of the input data.",
      "type": "wsid"
    }
  ]
}