details: http://www.bx.psu.edu/hg/galaxy/rev/50dbd8907d88 changeset: 2830:50dbd8907d88 user: jeremy goecks <jeremy.goecks@emory.edu> date: Mon Oct 05 17:39:29 2009 -0400 description: merge 0 file(s) affected in this change: diffs (35 lines): diff -r e6324f395d26 -r 50dbd8907d88 tools/filters/compare.xml --- a/tools/filters/compare.xml Mon Oct 05 17:38:54 2009 -0400 +++ b/tools/filters/compare.xml Mon Oct 05 17:39:29 2009 -0400 @@ -1,4 +1,4 @@ -<tool id="comp1" name="Compare two Queries"> +<tool id="comp1" name="Compare two Queries" version="1.0.1"> <description>to find common or distinct rows</description> <command interpreter="python">joinWrapper.py $input1 $input2 $field1 $field2 $mode $out_file1</command> <inputs> diff -r e6324f395d26 -r 50dbd8907d88 tools/filters/joinWrapper.py --- a/tools/filters/joinWrapper.py Mon Oct 05 17:38:54 2009 -0400 +++ b/tools/filters/joinWrapper.py Mon Oct 05 17:39:29 2009 -0400 @@ -22,8 +22,8 @@ try: #Sort the two files based on specified fields - os.system("sort -k %d -o %s %s" %(field1, tmpfile1.name, infile1)) - os.system("sort -k %d -o %s %s" %(field2, tmpfile2.name, infile2)) + os.system("sort -t $'\t' -k %d -o %s %s" %(field1, tmpfile1.name, infile1)) + os.system("sort -t $'\t' -k %d -o %s %s" %(field2, tmpfile2.name, infile2)) except Exception, exc: stop_err( 'Initialization error -> %s' %str(exc) ) @@ -40,9 +40,9 @@ break if mode == "V": - cmdline = 'join -v 1 -o %s -1 %d -2 %d %s %s | tr " " "\t" > %s' %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) + cmdline = "join -t $'\t' -v 1 -o %s -1 %d -2 %d %s %s > %s" %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) else: - cmdline = 'join -o %s -1 %d -2 %d %s %s | tr " " "\t" > %s' %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) + cmdline = "join -t $'\t' -o %s -1 %d -2 %d %s %s > %s" %(option, field1, field2, tmpfile1.name, tmpfile2.name, outfile) try: os.system(cmdline)