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"/>