#
# this VDL file will be run through the a preprocessor
# which converts certain keywords into replacements
#
# Configuration vars sampleSize=100000, proteinGroups=a:IVL.r:FYWH.p:KR.n:DE.t:GACS.d:TMQNP,
#   permsPerSet=20, numPerms=800, numMeasures=100,
#   workDir=gsiftp://pasoa-vmware.ecs.soton.ac.uk/home/vdt/vds/test/klaus/run,
#   sourceData=gsiftp://pasoa-vmware.ecs.soton.ac.uk/home/tester/klaus/samples/sample,
#   destDir=gsiftp://pasoa-vmware.ecs.soton.ac.uk/home/tester/klaus/run

TR tester::collateSample:1.0(input sessionID, output b )
{
  argument = "-x /home/tester/klaus/collateSample.sh";
  argument = " -s "${input:sessionID};
  argument = " -r LOCAL";
  argument = " 100000";
  argument = " "${output:b};
}
TR tester::gcode:1.0(input sessionID, input a, output b )
{
  argument = "-x /home/tester/klaus/gcode.sh";
  argument = " -s "${input:sessionID};
  argument = " -r LOCAL";
  argument = " a:IVL.r:FYWH.p:KR.n:DE.t:GACS.d:TMQNP";
  argument = " "${input:a};
  argument = " "${output:b};
}
TR tester::shuffle:1.0(input sessionID, input a, input count, output c )
{
  argument = "-x /home/tester/klaus/shuffle.sh";
  argument = " -s "${input:sessionID};
  argument = " -r LOCAL";
  argument = " "${input:a};
  argument = " "${input:count};
  argument = " "${output:c};
}
TR tester::measureWorkflow:1.0(input sessionID, input a, output b )
{
  argument = "-x /home/tester/klaus/measurement.sh";
  argument = " -s "${input:sessionID};
  argument = " -r LOCAL";
  argument = " "${input:a};
  argument = " "${output:b};
}
TR tester::nMeasuresWorkflow:1.0(input sessionID, input a, input start, input count, output c )
{
  argument = "-x /home/tester/klaus/Nmeasurements.sh";
  argument = " -s "${input:sessionID};
  argument = " -r LOCAL";
  argument = " "${input:a};
  argument = " "${input:start};
  argument = " "${input:count};
  argument = " "${output:c};
}
TR tester::compareSizes:1.0(input sessionID, input a[], output j )
{
  argument = "-x /home/tester/klaus/compareSizes.sh";
  argument = " -s "${input:sessionID};
  argument = " -r LOCAL";
  argument = " "${output:j};
  argument = " "${input:a};
}
TR tester::average:1.0(input sessionID, input a, output b )
{
  argument = "-x /home/tester/klaus/average.sh";
  argument = " -s "${input:sessionID};
  argument = " -r LOCAL";
  argument = " 20";
  argument = " "${input:a};
  argument = " "${output:b};
}

DV tester::collateSample:1.0->tester::collateSample:1.0,1.0(
   sessionID=@{input:"TestSession"},
   b=@{output:"sample.data"}
);
DV tester::gcode:1.0->tester::gcode:1.0,1.0(
   sessionID=@{input:"TestSession"},
   a=@{input:"sample.data"},
   b=@{output:"recoded.data"}
);

DV tester::measureWorkflow:1.0->tester::measureWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
   a=@{input:"recoded.data"},
   b=@{output:"sizes.data"}
);

DV tester::shuffle:1.0->tester::shuffle:1.0,1.0(
   sessionID=@{input:"TestSession"},
   a=@{input:"recoded.data"},
   count="800"
   c=@{output:"permutationList.data"}
);

  DV tester::nMeasuresWorkflow1:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="1",
     count="100",
     c=@{output:"nSizes1.data"}
  );
  DV tester::nMeasuresWorkflow101:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="101",
     count="100",
     c=@{output:"nSizes101.data"}
  );
  DV tester::nMeasuresWorkflow201:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="201",
     count="100",
     c=@{output:"nSizes201.data"}
  );
  DV tester::nMeasuresWorkflow301:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="301",
     count="100",
     c=@{output:"nSizes301.data"}
  );
  DV tester::nMeasuresWorkflow401:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="401",
     count="100",
     c=@{output:"nSizes401.data"}
  );
  DV tester::nMeasuresWorkflow501:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="501",
     count="100",
     c=@{output:"nSizes501.data"}
  );
  DV tester::nMeasuresWorkflow601:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="601",
     count="100",
     c=@{output:"nSizes601.data"}
  );
  DV tester::nMeasuresWorkflow701:1.0->tester::nMeasuresWorkflow:1.0,1.0(
   sessionID=@{input:"TestSession"},
     a=@{input:"permutationList.data"},
     start="701",
     count="100",
     c=@{output:"nSizes701.data"}
  );

DV tester::compareSizes:1.0->tester::compareSizes:1.0,1.0(
   sessionID=@{input:"TestSession"},
   a=[@{input:"sizes.data"},
@{input:"nSizes1.data"},
@{input:"nSizes101.data"},
@{input:"nSizes201.data"},
@{input:"nSizes301.data"},
@{input:"nSizes401.data"},
@{input:"nSizes501.data"},
@{input:"nSizes601.data"},
@{input:"nSizes701.data"}   ],
   j=@{output:"ComparativeSizes.data"}
);

DV tester::average:1.0->tester::average:1.0,1.0( 
   sessionID=@{input:"TestSession"},
   a=@{input:"ComparativeSizes.data"}, 
   b=@{output:"AveragedSizes.data"}
);

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