details: http://www.bx.psu.edu/hg/galaxy/rev/950a71339420 changeset: 1633:950a71339420 user: wychung date: Fri Nov 14 13:21:02 2008 -0500 description: update poisson test tool for R warnings.

2 file(s) affected in this change:

tools/taxonomy/poisson2test.py tools/taxonomy/poisson2test.xml

diffs (40 lines):

diff -r a5ec5ab6144b -r 950a71339420 tools/taxonomy/poisson2test.py --- a/tools/taxonomy/poisson2test.py Thu Nov 13 19:19:03 2008 -0500 +++ b/tools/taxonomy/poisson2test.py Fri Nov 14 13:21:02 2008 -0500 @@ -5,7 +5,7 @@ from rpy import *

-if ((len(sys.argv)-1) != 5): +if ((len(sys.argv)-1) != 6): print 'too few parameters' print 'usage: inputfile, col1, col2, d-value(not 0), p-val correction method(0 or 1)' sys.exit() @@ -21,6 +21,7 @@ j = int(sys.argv[3]) #second colum to compare d = float(sys.argv[4]) #correction factor k = int(sys.argv[5]) #p-val correction method + outfile = open(sys.argv[6],'w') # output data

if (i>j): print 'column order not correct col1 < col2' @@ -114,7 +115,7 @@

#printing all columns for n in range(fsize): - print "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n]) + print >> outfile, "%s\t%4.3f\t%4.3f\t%8.6f\t%8.6f\t%8.6f\t%8.6f" %(lines_arr[n].strip(),z1[n],z2[n],pz1[n],pz2[n],corrz1[n],corrz2[n])

diff -r a5ec5ab6144b -r 950a71339420 tools/taxonomy/poisson2test.xml --- a/tools/taxonomy/poisson2test.xml Thu Nov 13 19:19:03 2008 -0500 +++ b/tools/taxonomy/poisson2test.xml Fri Nov 14 13:21:02 2008 -0500 @@ -1,6 +1,6 @@ <tool id="poisson2test" name="Poisson two-sample test" version="1.0.0"> <description></description> - <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 > $output1 </command> + <command interpreter="python">poisson2test.py $input1 $input2 $input3 $input4 $input5 $output1 2>/dev/null </command> <inputs> <param name="input1" format="tabular" type="data" label="Input File"/> <param name="input2" type="integer" size="5" value="2" label="First Column"/>