view tools/metag_tools/convert_SOLiD_color2nuc.xml @ 1:cdcb0ce84a1b

author xuebing
date Fri, 09 Mar 2012 19:45:15 -0500
parents 9071e359b9a3
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<tool id="color2nuc" name="Convert Color Space" version="1.0.0">
<description> to Nucleotides </description>
<command interpreter="python"> $input1 $input2 $output1 </command>

    <param name="input1" type="data" format="txt" label="SOLiD color coding file" />
    <param name="input2" type="select" label="Keep prefix nucleotide">
    	<option value="yes">Yes</option>
    	<option value="no">No</option>
  	<data name="output1" format="fasta" />
		<param name="input1" value="convert_SOLiD_color2nuc_test1.txt" ftype="txt" />
		<param name="input2" value="no" />
		<output name="output1" file="convert_SOLiD_color2nuc_test1.out" />

.. class:: warningmark

The tool was designed for color space files generated from an ABI SOLiD sequencer. The file format must be fasta-like: the title starts with a ">" character, and each color space sequence starts with a leading nucleotide.

**What it does**

This tool converts a color space sequence to nucleotides. The leading character must be a nucleotide: A, C, G, or T. 


- If the color space file looks like this::

- If you would like to **keep** the leading nucleotide::

- If you **do not want to keep** the leading nucleotide (the length of nucleotide sequence will be one less than the color-space sequence)::


**ABI SOLiD Color Coding Alignment matrix**

 Each di-nucleotide is represented by a single digit: 0 to 3. The matrix is symmetric, thus the leading nucleotide is necessary to determine the sequence (otherwise there are four possibilities).

 .. image:: ./static/images/dualcolorcode.png