# HG changeset patch
# User jpayne
# Date 1559939058 14400
# Node ID eefafc5316981c8687abaa2820932a3466f2d438
# Parent  77d3edd25de7c68bb6cf698598e93dbd0b55df32
planemo upload

diff -r 77d3edd25de7 -r eefafc531698 SeqSero2/SeqSero2_package.py
--- a/SeqSero2/SeqSero2_package.py	Fri Jun 07 16:16:25 2019 -0400
+++ b/SeqSero2/SeqSero2_package.py	Fri Jun 07 16:24:18 2019 -0400
@@ -1312,7 +1312,7 @@
           predicted_serotype = "{}{}".format(predict_sero, star),
           note=claim.replace('\n','')
           )
-          result['*'] = star_line.replace('\t', ' ')
+          result['*'] = star_line.replace('\t', ' ').replace('\n','')
           with open("Seqsero_result.tsv","w") as new_file:
          #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##
          #new_file.close()
@@ -1370,7 +1370,7 @@
           predicted_serotype = "{}{}".format(predict_sero, star),
           note=claim.replace('\n','')
         )
-        result['*'] = star_line.replace('\t', ' ')
+        result['*'] = star_line.replace('\t', ' ').replace('\n','')
         with open("Seqsero_result.tsv","w") as new_file:
          #new_file.write("Output_directory:"+make_dir+"\nInput files:\t"+input_file+"\n"+"O antigen prediction:\t"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+highest_fliC+"\n"+"H2 antigen prediction(fljB):\t"+highest_fljB+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted subspecies:\t"+subspecies+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##
          #new_file.close()