# HG changeset patch
# User kellrott
# Date 1351727416 14400
# Node ID 01454ded89074145b4b40350977b4e070e2687c3

Uploaded

diff -r 000000000000 -r 01454ded8907 tabular_edit.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tabular_edit.xml	Wed Oct 31 19:50:16 2012 -0400
@@ -0,0 +1,115 @@
+<tool id="tabular_edit" name="Tabular Edit" version="1.0.0">
+	<description>Edit the contents and row/column labels of a tabular file using python statements</description>
+	<command interpreter="python">$script_file</command>
+	<inputs>
+		<param name="row_txt" type="text" area="True" size="5x35" label="Row Eval Code" optional="True">
+			<sanitizer>
+				<valid initial="string.printable">
+					<remove value="&quot;"/>
+				</valid>
+				<mapping initial="none">
+					<add source="&quot;" target="\&quot;"/>
+					<add source="\" target="\\"/>
+				</mapping>
+			</sanitizer>
+		</param>
+		<param name="col_txt" type="text" area="True" size="5x35" label="Column Eval Code" optional="True">
+			<sanitizer>
+				<valid initial="string.printable">
+					<remove value="&quot;"/>
+				</valid>
+				<mapping initial="none">
+					<add source="&quot;" target="\&quot;"/>
+				</mapping>
+			</sanitizer>
+		</param>
+		<param name="cell_txt" type="text" area="True" size="5x35" label="Cell Eval Code" optional="True">
+			<sanitizer>
+				<valid initial="string.printable">
+					<remove value="&quot;"/>
+				</valid>
+				<mapping initial="none">
+					<add source="&quot;" target="\&quot;"/>
+				</mapping>
+			</sanitizer>
+		</param>
+
+		<param name="matrix" type="data" format="tabular" label="Matrix"/>
+	</inputs>
+	<outputs>
+		<data format="tabular" name="outfile" />
+	</outputs>
+	<configfiles>
+        	<configfile name="script_file"><![CDATA[#!/usr/bin/env python
+import os
+import sys
+import csv
+import re
+import math
+
+def value_eval(code, value):
+    funcmap = {
+        "len":len,
+        "value" : value,
+        "re" : re,
+        "math" : math,
+        "float" : float
+    }
+    return str(eval(code,{"__builtins__":None},funcmap))
+
+
+row_text = """${row_txt}"""
+col_text = """${col_txt}"""
+cell_text = """${cell_txt}"""
+
+in_path = """${matrix}"""
+out_path = """${outfile}"""
+
+
+ohandle = open(out_path, "w")
+ihandle = open(in_path)
+reader = csv.reader(ihandle, delimiter="\t")
+writer = csv.writer(ohandle, delimiter="\t", lineterminator="\n")
+
+header = True
+for row in reader:
+    if header:
+        if len(col_text):
+            for i, val in enumerate(row[1:]):
+                row[i+1] = value_eval(col_text, val)
+        header = False
+    else:
+        if len(row_text):
+            row[0] = value_eval(row_text, row[0])
+      	if len(cell_text):
+      		for i in range(1,len(row)):
+      			row[i] = value_eval(cell_text,row[i])    
+    writer.writerow(row)
+
+ihandle.close()
+ohandle.close()
+
+
+]]></configfile>
+	</configfiles>
+	<help>
+This is a utility to perform editing operations on the contents and column/row labels of a tabular file.
+
+ - The 'Column Eval Code' operations occur on the first line.
+ - The 'Row Eval Code' operations occur on the first cell of every line
+ - The 'Cell Eval Code' operations occur on every non-label cell
+ - If any of the code blocks are empty, the operation is skipped 
+
+Example
+
+Remove the '.CEL' string from sample names::
+
+    re.sub(r'.CEL$', '', value)
+
+Log Transform the matrix cells::
+
+    math.log(float(value))
+
+
+	</help>
+</tool>