#
# this VDL file will be run through the a preprocessor
# which converts certain keywords into replacements
#
# Configuration vars sampleSize=$${sampleSize}, proteinGroups=$${proteinGroups},
#   permsPerSet=$${permsPerSet}, numPerms=$${numPerms}, numMeasures=$${numMeasures},
#   workDir=$${workDir},
#   sourceData=$${sourceData},
#   destDir=$${destDir}

TR tester::collateSample:1.0( output b )
{
  argument = " $${sampleSize}";
  argument = " "${output:b};
}
TR tester::gcode:1.0( input a, output b )
{
  argument = " $${proteinGroups}";
  argument = " "${input:a};
  argument = " "${output:b};
}
TR tester::shuffle:1.0( input a, input count, output c )
{
  argument = " "${input:a};
  argument = " "${input:count};
  argument = " "${output:c};
}
TR tester::measureWorkflow:1.0( input a, output b )
{
  argument = " "${input:a};
  argument = " "${output:b};
}
TR tester::nMeasuresWorkflow:1.0( input a, input start, input count, output c )
{
  argument = " "${input:a};
  argument = " "${input:start};
  argument = " "${input:count};
  argument = " "${output:c};
}
TR tester::compareSizes:1.0( input a[], output j )
{
  argument = " "${output:j};
  argument = " "${input:a};
}
TR tester::average:1.0( input a, output b )
{
  argument = " $${permsPerSet}";
  argument = " "${input:a};
  argument = " "${output:b};
}

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

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

DV tester::shuffle:1.0->tester::shuffle:1.0,1.0(
   a=@{input:"recoded.data"},
   count="$${numPerms}"
   c=@{output:"permutationList.data"}
);
MAP permutationList.data $${workDir}/permutationList.data

FOR permutation FROM 1 TO $${numPerms} STEP $${numMeasures}
  DV tester::nMeasuresWorkflow%permutation%:1.0->tester::nMeasuresWorkflow:1.0,1.0(
     a=@{input:"permutationList.data"},
     start="%permutation%",
     count="$${numMeasures}",
     c=@{output:"nSizes%permutation%.data"}
  );
  MAP permutation%permutation%.data $${workDir}/permutation%permutation%.data
  MAP nSizes%permutation%.data      $${workDir}/nSizes%permutation%.data
END

DV tester::compareSizes:1.0->tester::compareSizes:1.0,1.0(
   a=[@{input:"sizes.data"},
   LIST @{input:"nSizes%item%.data"} 1 $${numPerms} $${numMeasures}
   ],
   j=@{output:"ComparativeSizes.data"}
);
MAP ComparativeSizes.data $${workDir}/ComparativeSizes.data

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