type file;

(file phr, file pin, file psq) formatdb(file input) {
  app {
    formatdb "-i" @input;
  }
}

(file output) blast(file input1, file phr1, file pin1, file psq1, file input2, file phr2, file pin2, file psq2)
{
   app{
     blastall "-p" "blastp" "-d" @input1 "-i" @input2 "-m" "9" "-o" @output;
   } 
}

(file output) reciprocal(file reciprocalScript, file input1, file input2) {
  app {
    perl @reciprocalScript  "-i1" @input1 "-i2" @input2 "-o" 
@output;
  }
}

file reciprocalScript <"simple_reciprocal_best_hits.01b.pl">;

file input1  <"Ban.faa">;
file phr1 <"Ban.faa.phr">;
file pin1 <"Ban.faa.pin">;
file psq1 <"Ban.faa.psq">;

file input2  <"Bce.faa">;
file phr2 <"Bce.faa.phr">;
file pin2 <"Bce.faa.pin">;
file psq2 <"Bce.faa.psq">;

#file formatted1 <"Ban-db.faa">;
#file formatted2 <"Bce-db.faa">;

file output1 <"out.Bce2Ban.txt">;
file output2 <"out.Ban2Bce.txt">;
file output <"ortholog.pairs.txt">;

(phr1, pin1, psq1) = formatdb(input1);
(phr2, pin2, psq2) = formatdb(input2);

output1 = blast(input1, phr1, pin1, psq1, input2, phr2, pin2, psq2);
output2 = blast(input2, phr2, pin2, psq2, input1, phr1, pin1, psq1);
output = reciprocal(reciprocalScript, output1, output2);