<commit_before>{
  "name": "idr",
  "title": "IDR",
  "summary": "IDR Batch Consistency Analysis",
  "dxapi": "1.0.0",
  "version": "0.0.1",
  "categories": [
    "ENCODE Analysis Pipeline"
  ],
  "inputSpec": [
    {
      "name": "rep1_peaks",
      "label": "First replicate peak file",
      "class": "file",
      "optional": false
    },
    {
      "name": "rep2_peaks",
      "label": "Second replicate peak file",
      "class": "file",
      "optional": false
    },
    {
      "name": "pooled_peaks",
      "label": "Pooled replicates peak file",
      "class": "file",
      "optional": false
    },
    {
      "name": "idr_threshold",
      "label": "IDR threshold",
      "class": "float",
      "optional": true,
      "default": 0.02
    },
    {
      "name": "rank",
      "label": "Ranking measure",
      "class": "string",
      "optional": true,
      "default": "signal.value"
    }
  ],
  "outputSpec": [
    {
      "name": "EM_fit_output",
      "label": "The output from EM fitting",
      "class": "file",
      "optional": true
    },
    {
      "name": "empirical_curves_output",
      "label": "The output for plotting empirical curves",
      "class": "file",
      "optional": true
    },
    {
      "name": "EM_parameters_log",
      "label": "The parameters estimated from EM and the log of consistency analysis",
      "class": "file"
    },
    {
      "name": "npeaks_pass",
      "label": "File with the number of peaks that pass the IDR threshold for pairwise analysis",
      "class": "file"
    },
    {
      "name": "overlapped_peaks",
      "label": "The full set of peaks that overlap between the replicates with local and global IDR",
      "class": "file",
      "optional": true
    },
    {
      "name": "IDR_output",
      "label": "IDR output file",
      "class": "file"
    },
    {
      "name": "IDR_peaks",
      "label": "Final IDR thresholded file",
      "class": "file"
    },
    {
      "name": "N",
      "label": "The number of peaks that pass the IDR threshold for pairwise analysis",
      "class": "int"
    },
    {
      "name": "IDR2_plot",
      "label": "The plot from IDRv2",
      "class": "file",
      "optional": true
    }
  ],
  "runSpec": {
    "interpreter": "python2.7",
    "file": "src/idr.py",
    "systemRequirements": {
      "*": {"instanceType": "mem2_hdd2_x1"}
    }

  },
  "access": {
    "network": [
      "*"
    ]
  },
  "authorizedUsers": []
}
<commit_msg>Interactive mode for debugging<commit_after>{
  "name": "idr",
  "title": "IDR",
  "summary": "IDR Batch Consistency Analysis",
  "dxapi": "1.0.0",
  "version": "0.0.1",
  "categories": [
    "ENCODE Analysis Pipeline"
  ],
  "inputSpec": [
    {
      "name": "rep1_peaks",
      "label": "First replicate peak file",
      "class": "file",
      "optional": false
    },
    {
      "name": "rep2_peaks",
      "label": "Second replicate peak file",
      "class": "file",
      "optional": false
    },
    {
      "name": "pooled_peaks",
      "label": "Pooled replicates peak file",
      "class": "file",
      "optional": false
    },
    {
      "name": "idr_threshold",
      "label": "IDR threshold",
      "class": "float",
      "optional": true,
      "default": 0.02
    },
    {
      "name": "rank",
      "label": "Ranking measure",
      "class": "string",
      "optional": true,
      "default": "signal.value"
    },
    {
      "name": "interactive",
      "label": "Set up then hold for ssh interactive mode",
      "class": "boolean",
      "optional": true,
      "default": false
    }    
  ],
  "outputSpec": [
    {
      "name": "EM_fit_output",
      "label": "The output from EM fitting",
      "class": "file",
      "optional": true
    },
    {
      "name": "empirical_curves_output",
      "label": "The output for plotting empirical curves",
      "class": "file",
      "optional": true
    },
    {
      "name": "EM_parameters_log",
      "label": "The parameters estimated from EM and the log of consistency analysis",
      "class": "file"
    },
    {
      "name": "npeaks_pass",
      "label": "File with the number of peaks that pass the IDR threshold for pairwise analysis",
      "class": "file"
    },
    {
      "name": "overlapped_peaks",
      "label": "The full set of peaks that overlap between the replicates with local and global IDR",
      "class": "file",
      "optional": true
    },
    {
      "name": "IDR_output",
      "label": "IDR output file",
      "class": "file"
    },
    {
      "name": "IDR_peaks",
      "label": "Final IDR thresholded file",
      "class": "file"
    },
    {
      "name": "N",
      "label": "The number of peaks that pass the IDR threshold for pairwise analysis",
      "class": "int"
    },
    {
      "name": "IDR2_plot",
      "label": "The plot from IDRv2",
      "class": "file",
      "optional": true
    }
  ],
  "runSpec": {
    "interpreter": "python2.7",
    "file": "src/idr.py",
    "systemRequirements": {
      "*": {"instanceType": "mem2_hdd2_x1"}
    }

  },
  "access": {
    "network": [
      "*"
    ]
  },
  "authorizedUsers": []
}

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