<commit_before>{
    "author": {
        "name": "",
        "email": ""
    },
    "version": "1.0",
    "id": "pathiways",
    "name": "Pathiways",
    "description": "",
    "icon": {
        "size": "",
        "data": ""
    },
    "website": "http://",
    "publication": "",
    "globalParams": [],
    "executions": [{
        "id": "pathiways",
        "name": "Pathiways",
        "executable": "bin/pathiwaysANALYSIS.py --execution pathiways",
        "inputParams": [{"name":"norm-matrix", "dataType":"txt"},{"name":"exp-design", "dataType":"txt"}],
        "inputParamsFromTxt": [],
        "outputParam": "outdir",
        "validParams": [
            {"name":"norm-matrix", "description":"Normalized matrix file.", "required":"true"},
            {"name":"cel-compressed-file", "description":"ZIP Cel files", "required":"false"},
            {"name":"exp-design", "description":"Experimental design file.", "required":"true"},
            {"name":"pathways", "description":"List of pathways.", "required":"true"},
            {"name":"summ", "description":"Summ value.", "required":"true"},
            {"name":"control", "description":"Control value.", "required":"true"},
            {"name":"disease", "description":"Disease value.", "required":"true"},
            {"name":"platform", "description":"Platform value.", "required":"true"},
            {"name":"exp-name", "description":"Experiment name.", "required":"true"},
            {"name":"test", "description":"Comparison tests", "required":"true"},
            {"name":"paired", "description":"Wilcoxon comparison test can be paired or not", "required":"true"}
        ],
        "configAttr": [],
        "testCmd": "",
        "result": "pathiways"
    },
    {
         "id": "pathipred",
         "name": "Pathipred",
         "executable": "bin/pathiwaysANALYSIS.py --execution pathipred",
         "inputParams": [{"name":"norm-matrix", "dataType":"txt"},{"name":"exp-design", "dataType":"txt"}],
         "inputParamsFromTxt": [],
         "outputParam": "outdir",
         "validParams": [
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                   {"name":"cel-compressed-file", "description":"ZIP Cel files", "required":"false"},
                   {"name":"exp-design", "description":"Experimental design file.", "required":"true"},
                   {"name":"pathways", "description":"List of pathways.", "required":"true"},
                   {"name":"summ", "description":"Summ value.", "required":"true"},
                   {"name":"control", "description":"Control value.", "required":"true"},
                   {"name":"disease", "description":"Disease value.", "required":"true"},
                   {"name":"platform", "description":"Platform value.", "required":"true"},
                   {"name":"exp-name", "description":"Experiment name.", "required":"true"},
                   {"name":"k", "description":"k-fold", "required":"true"},
                   {"name":"expdesigntype", "description":"exp design type", "required":"true"}
         ],
         "configAttr": [],
         "testCmd": "",
         "result": "pathiways"
    },
    {
        "id": "pathipred-prediction",
        "name": "<NAME>",
        "executable": "bin/pathiwaysANALYSIS.py --execution pathipred-prediction",
        "inputParams": [{"name":"norm-matrix", "dataType":"txt"},{"name":"exp-design", "dataType":"txt"},{"name":"bestmodelfile","dataType":"txt"}],
        "inputParamsFromTxt": [],
        "outputParam": "outdir",
        "validParams": [
            {"name":"norm-matrix", "description":"Normalized matrix file.", "required":"true"},
            {"name":"cel-compressed-file", "description":"ZIP Cel files", "required":"false"},
            {"name":"exp-design", "description":"Experimental design file.", "required":"true"},
            {"name":"pathways", "description":"List of pathways.", "required":"true"},
            {"name":"summ", "description":"Summ value.", "required":"true"},
            {"name":"control", "description":"Control value.", "required":"true"},
            {"name":"disease", "description":"Disease value.", "required":"true"},
            {"name":"platform", "description":"Platform value.", "required":"true"},
            {"name":"expdesigntype", "description":"exp design type", "required":"true"},
            {"name":"bestmodelfile", "description":"best model file", "required":"true"},
            {"name":"exp-name", "description":"Experiment name.", "required":"true"}
        ],
        "configAttr": [],
        "testCmd": "",
        "result": "pathiways"
    }
],
    "examples": [],
    "acl": []
}
<commit_msg>updated pathivar manifest<commit_after>{
    "author": {
        "name": "",
        "email": ""
    },
    "version": "1.0",
    "id": "pathiways",
    "name": "Pathiways",
    "description": "",
    "icon": {
        "size": "",
        "data": ""
    },
    "website": "http://",
    "publication": "",
    "globalParams": [],
    "executions": [{
        "id": "pathiways",
        "name": "Pathiways",
        "executable": "bin/pathiwaysANALYSIS.py --execution pathiways",
        "inputParams": [{"name":"norm-matrix", "dataType":"txt"},{"name":"exp-design", "dataType":"txt"}],
        "inputParamsFromTxt": [],
        "outputParam": "outdir",
        "validParams": [
            {"name":"norm-matrix", "description":"Normalized matrix file.", "required":"true"},
            {"name":"cel-compressed-file", "description":"ZIP Cel files", "required":"false"},
            {"name":"exp-design", "description":"Experimental design file.", "required":"true"},
            {"name":"pathways", "description":"List of pathways.", "required":"true"},
            {"name":"summ", "description":"Summ value.", "required":"true"},
            {"name":"control", "description":"Control value.", "required":"true"},
            {"name":"disease", "description":"Disease value.", "required":"true"},
            {"name":"platform", "description":"Platform value.", "required":"true"},
            {"name":"exp-name", "description":"Experiment name.", "required":"true"},
            {"name":"test", "description":"Comparison tests", "required":"true"},
            {"name":"paired", "description":"Wilcoxon comparison test can be paired or not", "required":"true"}
        ],
        "configAttr": [],
        "testCmd": "",
        "result": "pathiways"
    },
    {
         "id": "pathipred",
         "name": "Pathipred",
         "executable": "bin/pathiwaysANALYSIS.py --execution pathipred",
         "inputParams": [{"name":"norm-matrix", "dataType":"txt"},{"name":"exp-design", "dataType":"txt"}],
         "inputParamsFromTxt": [],
         "outputParam": "outdir",
         "validParams": [
                   {"name":"norm-matrix", "description":"Normalized matrix file.", "required":"true"},
                   {"name":"cel-compressed-file", "description":"ZIP Cel files", "required":"false"},
                   {"name":"exp-design", "description":"Experimental design file.", "required":"true"},
                   {"name":"pathways", "description":"List of pathways.", "required":"true"},
                   {"name":"summ", "description":"Summ value.", "required":"true"},
                   {"name":"control", "description":"Control value.", "required":"true"},
                   {"name":"disease", "description":"Disease value.", "required":"true"},
                   {"name":"platform", "description":"Platform value.", "required":"true"},
                   {"name":"exp-name", "description":"Experiment name.", "required":"true"},
                   {"name":"k", "description":"k-fold", "required":"true"},
                   {"name":"expdesigntype", "description":"exp design type", "required":"true"},
                   {"name":"predmethod","description":"Prediction method","required":"true"}
         ],
         "configAttr": [],
         "testCmd": "",
         "result": "pathiways"
    },
    {
        "id": "pathipred-prediction",
        "name": "<NAME>",
        "executable": "bin/pathiwaysANALYSIS.py --execution pathipred-prediction",
        "inputParams": [{"name":"norm-matrix", "dataType":"txt"},{"name":"exp-design", "dataType":"txt"},{"name":"bestmodelfile","dataType":"txt"}],
        "inputParamsFromTxt": [],
        "outputParam": "outdir",
        "validParams": [
            {"name":"norm-matrix", "description":"Normalized matrix file.", "required":"true"},
            {"name":"cel-compressed-file", "description":"ZIP Cel files", "required":"false"},
            {"name":"exp-design", "description":"Experimental design file.", "required":"true"},
            {"name":"pathways", "description":"List of pathways.", "required":"true"},
            {"name":"summ", "description":"Summ value.", "required":"true"},
            {"name":"control", "description":"Control value.", "required":"true"},
            {"name":"disease", "description":"Disease value.", "required":"true"},
            {"name":"platform", "description":"Platform value.", "required":"true"},
            {"name":"expdesigntype", "description":"exp design type", "required":"true"},
            {"name":"bestmodelfile", "description":"best model file", "required":"true"},
            {"name":"exp-name", "description":"Experiment name.", "required":"true"}
        ],
        "configAttr": [],
        "testCmd": "",
        "result": "pathiways"
    },
    {
      "id": "pathivar",
      "name": "Pathivar",
      "executable": "bin/pathivarANALYSIS.py",
      "inputParams": [{"name":"vcfFile", "dataType":"txt"}],
      "inputParamsFromTxt": [],
      "outputParam": "outdir",
      "validParams": [
        {"name":"annotvcf", "description":"", "required":"false"},
        {"name":"vcfFile", "description":"", "required":"false"},
        {"name":"ctypes", "description":"", "required":"true"},
        {"name":"samplecol", "description":"", "required":"true"},
        {"name":"pathways", "description":"", "required":"true"},
        {"name":"tissue", "description":"", "required":"true"},
        {"name":"model", "description":"", "required":"true"},
        {"name":"comhom", "description":"", "required":"true"},
        {"name":"methodscore", "description":"", "required":"true"},
        {"name":"treshold", "description":"", "required":"true"},
	{"name":"tissueSet", "description":"", "required":"true"}
      ],
      "configAttr": [],
      "testCmd": "",
      "result": "pathiways"
    }
],
    "examples": [],
    "acl": []
}

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