--- a/sam2interval.py	Mon Aug 26 15:12:38 2013 -0400
+++ b/sam2interval.py	Wed Feb 05 06:58:53 2020 -0500
@@ -4,93 +4,95 @@
 import optparse
 import re
 
-def stop_err( msg ):
-    sys.stderr.write( msg )
-    sys.exit()
+
+def stop_err(msg):
+    sys.exit(msg)
+
 
 def main():
     usage = """%prog [options]
-    
+
 options (listed below) default to 'None' if omitted
     """
     parser = optparse.OptionParser(usage=usage)
 
     parser.add_option(
-        '-f','--input_sam_file',
+        '-f', '--input_sam_file',
         metavar="INPUT_SAM_FILE",
         dest='input_sam',
-        default = False,
+        default=False,
         help='Name of the SAM file to be filtered. STDIN is default')
-            
+
     parser.add_option(
-        '-c','--flag_column',
+        '-c', '--flag_column',
         dest='flag_col',
-        default = '2',
+        default='2',
         help='Column containing SAM bitwise flag. 1-based')
-        
+
     parser.add_option(
-        '-s','--start_column',
+        '-s', '--start_column',
         dest='start_col',
-        default = '4',
+        default='4',
         help='Column containing position. 1-based')
 
     parser.add_option(
-        '-g','--cigar_column',
+        '-g', '--cigar_column',
         dest='cigar_col',
-        default = '6',
+        default='6',
         help='Column containing CIGAR or extended CIGAR string')
 
     parser.add_option(
-        '-r','--ref_column',
+        '-r', '--ref_column',
         dest='ref_col',
-        default = '3',
+        default='3',
         help='Column containing name of the reference sequence coordinate. 1-based')
-        
+
     parser.add_option(
-        '-e','--read_column',
+        '-e', '--read_column',
         dest='read_col',
-        default = '1',
+        default='1',
         help='Column containing read name. 1-based')
 
     parser.add_option(
-        '-p','--print_all',
+        '-p', '--print_all',
         dest='prt_all',
         action='store_true',
-        default = False,
+        default=False,
         help='Print coordinates and original SAM?')
-    
+
     options, args = parser.parse_args()
 
     if options.input_sam:
-        infile = open ( options.input_sam, 'r')
+        infile = open(options.input_sam, 'r')
     else:
         infile = sys.stdin
 
-    cigar = re.compile( '\d+M|\d+N|\d+D|\d+P' )
+    cigar = re.compile('\d+M|\d+N|\d+D|\d+P')
 
-    print '#chrom\tstart\tend\tstrand\tread_name' # provide a (partial) header so that strand is automatically set in metadata
+    print('#chrom\tstart\tend\tstrand\tread_name')  # provide a (partial) header so that strand is automatically set in metadata
 
     for line in infile:
-        line = line.rstrip( '\r\n' )
-        if line and not line.startswith( '#' ) and not line.startswith( '@' ) :
-            fields = line.split( '\t' )
-            start = int( fields[ int( options.start_col ) - 1 ] ) - 1
+        line = line.rstrip('\r\n')
+        if line and not line.startswith('#') and not line.startswith('@'):
+            fields = line.split('\t')
+            start = int(fields[int(options.start_col) - 1]) - 1
             end = 0
-            for op in cigar.findall( fields[ int( options.cigar_col) - 1 ] ):
-                end += int( op[ 0:len( op ) - 1 ] )
-                
-            strand = '+' 
-            if bool( int( fields[ int( options.flag_col ) - 1 ] ) & 0x0010 ):
+            for op in cigar.findall(fields[int(options.cigar_col) - 1]):
+                end += int(op[0:len(op) - 1])
+
+            strand = '+'
+            if bool(int(fields[int(options.flag_col) - 1]) & 0x0010):
                 strand = '-'
-            read_name = fields[ int( options.read_col ) - 1 ]
-            ref_name  = fields[ int( options.ref_col ) - 1 ]
-            
+            read_name = fields[int(options.read_col) - 1]
+            ref_name = fields[int(options.ref_col) - 1]
+
             if ref_name != '*':
-                # Do not print lines with unmapped reads that contain '*' instead of chromosome name        
-                if options.prt_all: 
-                    print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, line)
+                # Do not print lines with unmapped reads that contain '*' instead of chromosome name
+                if options.prt_all:
+                    print('%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end + start), strand, line))
                 else:
-                    print '%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end+start), strand, read_name)
+                    print('%s\t%s\t%s\t%s\t%s' % (ref_name, str(start), str(end + start), strand, read_name))
+
 
-if __name__ == "__main__": main()
-
+if __name__ == "__main__":
+    main()

--- a/sam2interval.xml	Mon Aug 26 15:12:38 2013 -0400
+++ b/sam2interval.xml	Wed Feb 05 06:58:53 2020 -0500
@@ -1,6 +1,10 @@
-<tool id="sam2interval" name="Convert SAM" version="1.0.1">
+<tool id="sam2interval" name="Convert SAM" version="1.0.2" profile="16.04">
   <description>to interval</description>
-  <command interpreter="python">sam2interval.py --input_sam_file=$input1 $print_all > $out_file1
+  <requirements>
+    <requirement type="package" version="3.7">python</requirement>
+  </requirements>
+  <command>
+    python '$__tool_directory__/sam2interval.py' --input_sam_file='$input1' $print_all > '$out_file1'
   </command>
   <inputs>
     <param format="sam" name="input1" type="data" label="Select dataset to convert"/>