changeset 1:26d0d9bdbafc draft

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit dc2e3b631f515e905d5645baa4fb49df8e8cc0d5"

--- a/mergeCols.py	Mon Nov 09 11:45:18 2015 -0500
+++ b/mergeCols.py	Wed Jun 03 14:22:15 2020 +0000
@@ -1,37 +1,36 @@
-import sys, re
+import sys
 
-def stop_err( msg ):
-    sys.stderr.write( msg )
-    sys.exit()
 
 def __main__():
     try:
-        infile =  open ( sys.argv[1], 'r')
-        outfile = open ( sys.argv[2], 'w')
-    except:
-        stop_err( 'Cannot open or create a file\n' )
-        
-    if len( sys.argv ) < 4:
-        stop_err( 'No columns to merge' )
+        infile = open(sys.argv[1], 'r')
+        outfile = open(sys.argv[2], 'w')
+    except Exception:
+        sys.exit('Cannot open or create a file\n')
+
+    if len(sys.argv) < 4:
+        sys.exit('No columns to merge\n')
     else:
-        cols = sys.argv[3:]        
+        cols = sys.argv[3:]
 
     skipped_lines = 0
 
     for line in infile:
-        line = line.rstrip( '\r\n' )
-        if line and not line.startswith( '#' ):
-            fields = line.split( '\t' )
+        line = line.rstrip('\r\n')
+        if line and not line.startswith('#'):
+            fields = line.split('\t')
             line += '\t'
             for col in cols:
                 try:
-                    line += fields[ int( col ) -1 ]
-                except:
+                    line += fields[int(col) - 1]
+                except Exception:
                     skipped_lines += 1
-                    
-            print >>outfile, line
-            
+
+            print(line, file=outfile)
+
     if skipped_lines > 0:
-        print 'Skipped %d invalid lines' % skipped_lines
-            
-if __name__ == "__main__" : __main__()
\ No newline at end of file
+        print('Skipped %d invalid lines' % skipped_lines)
+
+
+if __name__ == "__main__":
+    __main__()

--- a/mergeCols.xml	Mon Nov 09 11:45:18 2015 -0500
+++ b/mergeCols.xml	Wed Jun 03 14:22:15 2020 +0000
@@ -1,5 +1,8 @@
-<tool id="mergeCols1" name="Merge Columns" version="1.0.1">
+<tool id="mergeCols1" name="Merge Columns" version="1.0.2">
   <description>together</description>
+  <requirements>
+    <requirement type="package" version="3.7">python</requirement>
+  </requirements>
   <command interpreter="python">
    mergeCols.py 
       "${input1}"