# HG changeset patch
# User dave
# Date 1553106512 14400
# Node ID d2aa2a22721de69e24309603d7f4c0b009cf5c4a
# Parent  3e9704b9d49e9dcba46f0b534c6a29db35c0d1e9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abayesqr commit f009487e8fec49f10396185ffd2fc4fe65bf4f29-dirty

diff -r 3e9704b9d49e -r d2aa2a22721d abayesqr.xml
--- a/abayesqr.xml	Wed Mar 20 13:08:41 2019 -0400
+++ b/abayesqr.xml	Wed Mar 20 14:28:32 2019 -0400
@@ -8,7 +8,7 @@
         ln -s '$reference' input.fasta &&
         ln -s '$input' input.sam &&
         aBayesQR $abayes_params &&
-        python $__tool_directory__/parse_output.py
+        python '$__tool_directory__/parse_output.py'
         ]]>
     </command>
     <configfiles>
diff -r 3e9704b9d49e -r d2aa2a22721d parse_output.py
--- a/parse_output.py	Wed Mar 20 13:08:41 2019 -0400
+++ b/parse_output.py	Wed Mar 20 14:28:32 2019 -0400
@@ -1,9 +1,11 @@
+import os
 from Bio.Seq import Seq
 from Bio.SeqRecord import SeqRecord
 from Bio import SeqIO
 
 def parse_abayesqr_output(input_text, output_fasta):
-    with open(input_text) as input_file:
+    wd = os.getcwd()
+    with open(os.path.join(wd, input_text)) as input_file:
         lines = input_file.readlines()
     records = []
     for i, line in enumerate(lines):
@@ -15,7 +17,7 @@
             seq = Seq(line.strip())
             record = SeqRecord(seq, id=header, description='')
             records.append(record)
-    SeqIO.write(records, output_fasta, 'fasta')
+    SeqIO.write(records, os.path.join(wd, output_fasta), 'fasta')
 
 if __name__ == '__main__':
     parse_abayesqr_output("test_ViralSeq.txt", "haplotypes.fasta")