# HG changeset patch
# User drosofff
# Date 1458595957 14400
# Node ID c1ab6747fb6679806809e367b41918dbb3c7e33b
# Parent  4c60ceadc414f25c299869e4a86ef5440757e02a
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 0651eb8c86d890e4b223fec82ab3980932710030

diff -r 4c60ceadc414 -r c1ab6747fb66 sam_to_fastq.py
--- a/sam_to_fastq.py	Mon Mar 21 14:40:06 2016 -0400
+++ b/sam_to_fastq.py	Mon Mar 21 17:32:37 2016 -0400
@@ -15,18 +15,18 @@
         
 def print_fastq_sequence(samline, file):
   samfields = samline[:-1].split("\t")
-  print >> file, '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10])
+  file.write ( '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10]) )
 
 def main(input, output):
     infile = open (input, "r")
     outfile = open (output, "w")
-    for line in infile:
-        if line[0] == "@":
-            continue
-        if line.split("\t")[1] != "4":
-            print_fastq_sequence (line, outfile)
-    infile.close()
-    outfile.close()
+    with open (input, "r") as infile:
+        with open (output, "w") as outfile:
+            for line in infile:
+                if line[0] == "@":
+                    continue
+                if line.split("\t")[1] != "4":
+                    print_fastq_sequence (line, outfile)
 
 if __name__ == "__main__":
     args = Parser()
diff -r 4c60ceadc414 -r c1ab6747fb66 sam_to_fastq.xml
--- a/sam_to_fastq.xml	Mon Mar 21 14:40:06 2016 -0400
+++ b/sam_to_fastq.xml	Mon Mar 21 17:32:37 2016 -0400
@@ -11,7 +11,7 @@
 
     <tests>
         <test>
-            <param ftype="fasta" name="input" value="input.sam" />
+            <param ftype="sam" name="input" value="input.sam" />
             <output file="output.fastq" name="output" />
         </test>
     </tests>