annotate tabular_edit.xml @ 0:01454ded8907 draft default tip

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<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>