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

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{
  "name": "mhplot",
  "title": "Manhattan Plot",
  "summary": "Generates a Manhattan plot from the data provided. This app acts as a wrapper for the 'manhattan' function from the R package 'qqman'. Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).",
  "dxapi": "1.0.0",
  "inputSpec": [
    {
      "name": "datafile",
      "label": "Required: data files",
      "class": "array:file",
      "optional": false
    },
    {
      "name": "snpinfofile",
      "label": "Optional: SNPInfo files",
      "class": "array:file",
      "optional": true
    },
    {
      "name": "label",
      "label": "Filename prefix label",
      "class": "string",
      "optional": true,
      "default": "results"
    },
    {
      "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": "p_col",
      "label": "P-value column name. Must be the same if plotting multiple datasets (e.g. merging chromosomes).",
      "class": "string",
      "optional": true,
      "default": "p"
    },
    {
      "name": "gene_col",
      "label": "Gene column name. Not currently used.",
      "class": "string",
      "optional": true,
      "default": "gene"
    },
    {
      "name": "chr_col",
      "label": "Chromosome column name. If missing, script will derive it from snpname if the format is CHR:POS.",
      "class": "string",
      "optional": true,
      "default": "chr"
    },
    {
      "name": "pos_col",
      "label": "Position column name. If missing, script will derive it from snpname if the format is CHR:POS.",
      "class": "string",
      "optional": true,
      "default": "pos"
    },
    {
      "name": "snp_col",
      "label": "SNPname column name.",
      "class": "string",
      "optional": true,
      "default": "Name"
    },
    {
      "name": "chr_labels",
      "label": "chr_labels: A character vector equal to the number of chromosomes specifying the chromosome labels (e.g., 'c(1:22, 'X', 'Y', 'MT')').",
      "class": "string",
      "optional": true,
      "default": "NULL"
    },
    {
      "name": "filter",
      "label": "filter: Filtering string to subset the data. Ex: 'maf>0.05' or 'p<=0.01'",
      "class": "string",
      "optional": true,
      "default": "p>0"
    },
    {
      "name": "mh_color",
      "label": "Vector of colors, either by color name or 6-digit hex value.",
      "class": "array:string",
      "optional": true,
      "default": [
        "gray50",
        "black"
      ]
    },
    {
      "name": "main_title",
      "label": "main: The title of the Manhattan plot.",
      "class": "string",
      "optional": true,
      "default": "Manhattan Plot"
    },
    {
      "name": "suggestive_line",
      "label": "Where to draw a 'suggestive' line. Default -log10(1e-5). Set to 'FALSE' to disable.",
      "class": "string",
      "optional": true,
      "default": "-log10(1e-5)"
    },
    {
      "name": "genomewide_line",
      "label": "Where to draw a 'genome-wide significant' line. Default -log10(5e-8). Set to 'FALSE' to disable.",
      "class": "string",
      "optional": true,
      "default": "-log10(5e-8)"
    },
    {
      "name": "highlight",
      "label": "Highlighted Areas: A list of names from your 'gene' column to highlight, for example 'gene1,gene2,gene3'",
      "class": "array:string",
      "optional": true,
      "default": [
        "NULL"
      ]
    },
    {
      "name": "logp",
      "label": "logp: If TRUE, the -log10 of the p-value is plotted. It isn't very useful to plot raw p-values, but plotting the raw value could be useful for other genome-wide plots, for example, peak heights, bayes factors, test statistics, other 'scores', etc.",
      "class": "string",
      "optional": true,
      "default": "TRUE"
    }
  ],
  "outputSpec": [
    {
      "name": "mhplot",
      "label": "Output Manhattan plot",
      "class": "file"
    }
  ],
  "runSpec": {
    "systemRequirements": {
      "process": {
        "instanceType": "mem3_ssd1_x4"
      },
      "main": {
        "instanceType": "mem3_ssd1_x4"
      },
      "*": {
        "instanceType": "mem3_ssd1_x4"
      }
    },
    "file": "src/code.sh",
    "interpreter": "bash"
  },
  "access": {
    "project": "CONTRIBUTE",
    "allProjects": "CONTRIBUTE",
    "network": [
      "*"
    ]
  }
}