{
  "sbg:id": "rnaseqGene",
  "id": "#rnaseqGene",
  "inputs": [
    {
      "type": [
        {
          "items": "File",
          "type": "array"
        }
      ],
      "label": "bam files",
      "description": "a list of bam files",
      "streamable": false,
      "default": "",
      "id": "#bamfiles",
      "inputBinding": {
        "position": 0,
        "prefix": "--bamfiles",
        "separate": true,
        "itemSeparator": ",",
        "sbg:cmdInclude": true
      },
      "required": false
    },
    {
      "type": [
        "File"
      ],
      "label": "design matrix",
      "description": "",
      "streamable": false,
      "default": "",
      "id": "#design",
      "inputBinding": {
        "position": 0,
        "prefix": "--design",
        "separate": true,
        "sbg:cmdInclude": true
      },
      "required": false
    },
    {
      "type": [
        "File"
      ],
      "label": "gene feature files",
      "description": "",
      "streamable": false,
      "default": "",
      "id": "#gtffile",
      "inputBinding": {
        "position": 0,
        "prefix": "--gtffile",
        "separate": true,
        "sbg:cmdInclude": true
      },
      "sbg:stageInput": "copy",
      "required": false
    },
    {
      "type": [
        "null",
        {
          "name": "format",
          "symbols": ["pdf", "html"],
          "type": "enum"
        }
      ],
      "label": "report foramt html or pdf",
      "description": "",
      "streamable": false,
      "default": "",
      "id": "#format",
      "inputBinding": {
        "position": 0,
        "prefix": "--format",
        "separate": true,
        "sbg:cmdInclude": true
      },
      "required": false
    }
  ],
  "outputs": [
    {
      "type": ["null", "File"],
      "label": "report",
      "description": "A reproducible report created by Rmarkdown",
      "streamable": false,
      "default": "",
      "id": "#report",
      "outputBinding": {
        "glob": {
          "engine": "#cwl-js-engine",
          "script": "x = $job[['inputs']][['format']];\n                                                  if(x == 'undefined' || x == null){\n                                                   x = 'html';\n                                                    };\n                                                  'rnaseqGene.' +  x",
          "class": "Expression"
        }
      }
    },
    {
      "type": ["null", "File"],
      "label": "heatmap",
      "description": "A heatmap plot to show the Euclidean distance between samples",
      "streamable": false,
      "default": "",
      "id": "#heatmap",
      "outputBinding": {
        "glob": "heatmap.pdf"
      }
    },
    {
      "type": ["null", "File"],
      "label": "count",
      "description": "Reads counts matrix",
      "streamable": false,
      "default": "",
      "id": "#count",
      "outputBinding": {
        "glob": "count.csv"
      }
    },
    {
      "type": ["null", "File"],
      "label": "Differential expression table",
      "description": "Differential expression table",
      "streamable": false,
      "default": "",
      "id": "#de",
      "outputBinding": {
        "glob": "de.csv"
      }
    }
  ],
  "requirements": [],
  "hints": [
    {
      "class": "DockerRequirement",
      "dockerPull": "tengfei/rnaseqgene",
      "dockerLoad": "",
      "dockerFile": "",
      "dockerImageId": "",
      "dockerOutputDirectory": ""
    },
    {
      "class": "sbg:CPURequirement",
      "value": 1
    },
    {
      "class": "sbg:MemRequirement",
      "value": 2000
    }
  ],
  "label": "rnaseqgene",
  "description": "A RNA-seq Differiencial Expression Flow and Report",
  "class": "CommandLineTool",
  "baseCommand": [
    "performDE.R"
  ],
  "arguments": []
}
