--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalize_dataset.py	Tue Apr 12 03:08:08 2016 -0400
@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import re
+
+def isfloat(value):
+  try:
+    float(value)
+    return True
+  except ValueError:
+    return False
+
+def normalize_dataset(args):
+    with open(args.input_file, 'r') as input_file:
+        input_file_content = input_file.readlines()
+        if args.normalization == 'column':
+            column_number = len(input_file_content[0][:-1].split('\t'))
+            column_sum = [0] * column_number
+
+        with open(args.output_file, 'w') as output_file:
+            for line in input_file_content:
+                split_line = line[:-1].split('\t')
+
+                if args.normalization == 'row':
+                    row_sum = 0
+
+                    for col in split_line:
+                        if isfloat(col):
+                            row_sum += float(col) 
+
+                    sep = ''
+                    for col in split_line:
+                        if isfloat(col):
+                            if args.format == 'percentage':
+                                output_file.write(sep + str(float(col)/row_sum))
+                            else:
+                                output_file.write(sep + str(100*float(col)/row_sum))
+                        else:
+                            output_file.write(sep + col)
+                        sep = '\t'
+                    output_file.write('\n')
+
+                elif args.normalization == 'column':
+                    for i in range(len(split_line)):
+                        if isfloat(split_line[i]):
+                            column_sum[i] += float(split_line[i]) 
+
+            if args.normalization == 'column':
+                for line in input_file_content:
+                    split_line = line[:-1].split('\t')
+                    sep = ''
+                    for i in range(len(split_line)):
+                        if isfloat(split_line[i]):
+                            if args.format == 'percentage':
+                                output_file.write(sep + str(100*float(split_line[i])/column_sum[i]))
+                            else:
+                                output_file.write(sep + str(float(split_line[i])/column_sum[i]))
+                        else:
+                            output_file.write(sep + split_line[i])
+                        sep = '\t'
+                    output_file.write('\n')
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input_file', required=True)
+    parser.add_argument('--output_file', required=True)
+    parser.add_argument('--normalization', required=True, 
+        choices= ['column','row'])
+    parser.add_argument('--format', required=True, 
+        choices= ['proportion','percentage'])
+    args = parser.parse_args()
+    normalize_dataset(args)
\ No newline at end of file

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/normalize_dataset.xml	Tue Apr 12 03:08:08 2016 -0400
@@ -0,0 +1,53 @@
+<tool id="normalize_dataset" name="Normalize a dataset by" version="0.1.0">
+    <description>row or column sum</description>
+
+    <requirements>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        python $__tool_directory__/normalize_dataset.py
+            --input_file $input_file
+            --output_file $output_file
+            --normalization $normalization
+            --format $format
+    ]]></command>
+
+    <inputs>
+        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
+
+        <param name="normalization" label="Normalization on" type="select" help="(--normalization)">
+            <option value="column" selected="True">Column</option>
+            <option value="row">Row</option>
+        </param>
+
+        <param name="format" label="Output format" type="select" help="(--format)">
+            <option value="proportion" selected="True">Proportion</option>
+            <option value="percentage">Percentage</option>
+        </param>
+    </inputs>
+
+    <outputs>
+        <data name="output_file" format="tabular"
+            label="${tool.name} on ${on_string}: Normalized dataset" />
+    </outputs>
+
+    <tests>
+    </tests>
+
+    <help><![CDATA[
+        **What it does**
+
+        This tool normalizes each row or column of a dataset by the row or column sum.
+
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
\ No newline at end of file