assocplot/dxapp.json at master · AnalysisCommons/assocplot · GitHub

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{
  "name": "assocplot",
  "title": "Regional association plot",
  "summary": "assocplot",
  "dxapi": "1.0.0",
  "inputSpec": [
    {
      "name": "datafile",
      "label": "Required: datafile",
      "class": "file",
      "optional": false
    },
    {
      "name": "ldfile",
      "label": "Required: ldfile",
      "class": "file",
      "optional": false
    },
    {
      "name": "label",
      "label": "Label: Enter a prefix for your output plot (no spaces).",
      "class": "string",
      "optional": true,
      "default": "test"
    },
    {
      "name": "output_type",
      "label": "The filetype of the output plot. Must choose 'png', 'tiff', or 'pdf'.",
      "class": "string",
      "optional": true,
      "default": "png",
      "choices": [
        "png",
        "tiff",
        "pdf"
      ]
    },
    {
      "name": "output_args",
      "label": "Optional arguments for graphics function: eg. width, height, res, ppi, units, etc.",
      "class": "string",
      "optional": true,
      "default": ""
    },
    {
      "name": "traitname",
      "label": "Optional name of trait to appear in plot title. Ex: LDL, SBP, etc.",
      "class": "string",
      "optional": true,
      "default": ""
    },
    {
      "name": "groupname",
      "label": "Optional group/project name to appear in plot title. Ex: CHARGE, CHARGE-T2D, TOPMED, etc.",
      "class": "string",
      "optional": true,
      "default": ""
    },
    {
      "name": "ld_filetype",
      "label": "The format of the LD file. PLINK or Haploview supported at this time.",
      "class": "string",
      "optional": true,
      "default": "PLINK",
      "choices": [
        "PLINK",
        "Haploview"
      ]
    },
    {
      "name": "snp_col",
      "label": "Marker column name",
      "class": "string",
      "optional": true,
      "default": "Name"
    },
    {
      "name": "gene_col",
      "label": "Gene (or other form of aggregation) column name",
      "class": "string",
      "optional": true,
      "default": "gene"
    },
    {
      "name": "chr_col",
      "label": "Chromosome column name",
      "class": "string",
      "optional": true,
      "default": "chr"
    },
    {
      "name": "pos_col",
      "label": "Position column name",
      "class": "string",
      "optional": true,
      "default": "pos"
    },
    {
      "name": "p_col",
      "label": "P-value column name",
      "class": "string",
      "optional": true,
      "default": "p"
    },
    {
      "name": "freq_col",
      "label": "Frequency column name",
      "class": "string",
      "optional": true,
      "default": "maf"
    },
    {
      "name": "hetdf_col",
      "label": "HetDF column name",
      "class": "string",
      "optional": true,
      "default": "HetDF"
    },
    {
      "name": "index_snp",
      "label": "Index SNP (chr:pos) in the specific region to display.",
      "class": "string",
      "optional": true,
      "default": ""
    },
    {
      "name": "index_gene",
      "label": "Index gene in the specific region to display.",
      "class": "string",
      "optional": true,
      "default": ""
    },
    {
      "name": "index_region",
      "label": "Index region to display. Ex: '16:100000,16:200000'",
      "class": "string",
      "optional": true,
      "default": ""
    },
    {
      "name": "region_width",
      "label": "Width of window around index SNP. Default 500kb.",
      "class": "string",
      "optional": true,
      "default": "500000"
    },
    {
      "name": "ancestry",
      "label": "Ancestry group (AFR or CEU)",
      "class": "string",
      "optional": true,
      "default": "CEU",
      "choices": [
        "AFR",
        "CEU"
      ]
    },
    {
      "name": "chr",
      "label": "Chromosome number",
      "class": "string",
      "optional": false
    }
  ],
  "outputSpec": [
    {
      "name": "assoc_plot",
      "label": "regional_association.png",
      "class": "file"
    }
  ],
  "runSpec": {
    "systemRequirements": {
      "*": {
        "instanceType": "mem2_hdd2_x2"
      }
    },
    "file": "src/code.sh",
    "interpreter": "bash"
  },
  "access": {
    "project": "CONTRIBUTE",
    "allProjects": "CONTRIBUTE",
    "network": [
      "*"
    ]
  }
}