outputfile += '\n'
if (t.apply_calc == 'QuEST' or t.apply_calc == 'WingPeaks' or t.apply_calc == 'MACS'):
outputfile += '\n<PeakCalling TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Caller="'+t.apply_calc+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
- outputfile += '\n<Signal Library="'+t.subject1.library_id+'"/>'
- outputfile += '\n<Background Library="'+t.subject2.library_id+'"/>'
+ if t.subject1:
+ outputfile += '\n<Signal Library="'+t.subject1.library_id+'"/>'
+ if t.subject2:
+ outputfile += '\n<Background Library="'+t.subject2.library_id+'"/>'
+ else:
+ outputfile += '\n<Err>Background Library Missing</Err>'
+ else:
+ outputfile += '\n<Err>Signal Library Missing</Err>'
+ outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
outputfile += '\n</PeakCalling>'
+
+ if (t.apply_calc == 'Methylseq'):
+ outputfile += '\n<Methylseq TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
+ if t.subject1:
+ outputfile += '\n<Hpa2 Library="'+t.subject1.library_id+'"/>'
+ if t.subject2:
+ outputfile += '\n<Msp1 Library="'+t.subject2.library_id+'"/>'
+ else:
+ outputfile += '\n<Err>Msp1 Library Missing</Err>'
+ else:
+ outputfile += '\n<Err>Hpa2 Library Missing</Err>'
+ outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
+ outputfile += '\n</Methylseq>'
if (t.apply_calc == 'ProfileReads' or t.apply_calc == 'qPCR'):
outputfile += '\n<'+t.apply_calc+' TaskId="'+t.id.__str__()+'" Name="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'" Library="'+t.subject1.library_id+'"/>'
if (t.apply_calc == 'CompareLibs'):
outputfile += '\n<CompareLibraries TaskId="'+t.id.__str__()+'" TF="'+t.task_name+'" Genome="'+t.subject1.library_species.use_genome_build+'">'
- outputfile += '\n<Library Library="'+t.subject1.library_id+'"/>'
- outputfile += '\n<Library Library="'+t.subject2.library_id+'"/>'
+ if t.subject1:
+ outputfile += '\n<Library Library="'+t.subject1.library_id+'"/>'
+ else:
+ outputfile += '\n<Err>Library Missing</Err>'
+ if t.subject2:
+ outputfile += '\n<Library Library="'+t.subject2.library_id+'"/>'
+ else:
+ outputfile += '\n<Err>Library Missing</Err>'
+ outputfile += '\n<params>'+t.task_params.__str__()+'</params>'
outputfile += '\n</CompareLibraries>'
#if (t.apply_calc == 'ComparePeakCalls'):