{"description":"A simple accuracy test. Run for each bowtie version separately.",
 "name" : "Acc_1",
 "tests": [
    {"description":"An accuracy test.",
     "name":"pair wise accuracy",
     "input_data":{
            "files": [
                 "hg19.1.bt2",
                 "hg19.2.bt2",
                 "hg19.3.bt2",
                 "hg19.4.bt2",
                 "hg19.rev.1.bt2",
                 "hg19.rev.2.bt2",
                 "hg19.fa",
                 "art_150_mil_1.fq",
                 "art_150_mil_2.fq"
            ],
            "loading":[ " ln -s ../work/genomes/human_hg19/hg19.fa ##DATADIR##/",
                        " ln -s ../work/genomes/human_hg19/hg19.1.bt2 ##DATADIR##/",
                        " ln -s ../work/genomes/human_hg19/hg19.2.bt2 ##DATADIR##/",
                        " ln -s ../work/genomes/human_hg19/hg19.3.bt2 ##DATADIR##/",
                        " ln -s ../work/genomes/human_hg19/hg19.4.bt2 ##DATADIR##/",
                        " ln -s ../work/genomes/human_hg19/hg19.rev.1.bt2 ##DATADIR##/",
                        " ln -s ../work/genomes/human_hg19/hg19.rev.2.bt2 ##DATADIR##/",
                        "art_illumina -sam -mp -l 150 -m 200 -s 10 -o ##DATADIR##/art_150 -f 5 -i ##DATADIR##/hg19.fa -rs 1415911971",
                        "cat ##DATADIR##/art_1501.fq | head -4000000 > ##DATADIR##/art_150_mil_1.fq",
                        "cat ##DATADIR##/art_1502.fq | head -4000000 > ##DATADIR##/art_150_mil_2.fq"
             ] 
      },
     "runable":{
            "program":"bowtie2",
            "options":[
                "-x ##DATADIR##/hg19",
                "-1 ##DATADIR##/art_150_mil_1.fq",
                "-2 ##DATADIR##/art_150_mil_2.fq",
                "-S ##OUTDIR##/accuracy.sam" 
            ],
            "parameters":[],
            "outfiles":["##OUTDIR##/accuracy.sam"]
       },
     "metric":"TestAccuracy"
    }
 ]
}
