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1 <tool id="color2nuc" name="Convert Color Space" version="1.0.0">
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2 <description> to Nucleotides </description>
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3 <command interpreter="python">convert_SOLiD_color2nuc.py $input1 $input2 $output1 </command>
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4
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5 <inputs>
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6 <param name="input1" type="data" format="txt" label="SOLiD color coding file" />
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7 <param name="input2" type="select" label="Keep prefix nucleotide">
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8 <option value="yes">Yes</option>
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9 <option value="no">No</option>
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10 </param>
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11 </inputs>
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12 <outputs>
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13 <data name="output1" format="fasta" />
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14 </outputs>
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15 <!--
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16 <tests>
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17 <test>
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18 <param name="input1" value="convert_SOLiD_color2nuc_test1.txt" ftype="txt" />
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19 <param name="input2" value="no" />
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20 <output name="output1" file="convert_SOLiD_color2nuc_test1.out" />
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21 </test>
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22 </tests>
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23 -->
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24 <help>
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25
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26 .. class:: warningmark
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27
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28 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.
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29
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30 -----
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31
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32 **What it does**
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33
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34 This tool converts a color space sequence to nucleotides. The leading character must be a nucleotide: A, C, G, or T.
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35
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36 -----
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37
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38 **Example**
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39
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40 - If the color space file looks like this::
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41
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42 >seq1
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43 A013
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44 >seq2
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45 T011213122200221123032111221021210131332222101
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46
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47 - If you would like to **keep** the leading nucleotide::
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48
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49 >seq1
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50 AACG
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51 >seq2
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52 TTGTCATGAGAAAGACAGCCGACACTCAAGTCAACGTATCTCTGGT
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53
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54 - If you **do not want to keep** the leading nucleotide (the length of nucleotide sequence will be one less than the color-space sequence)::
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55
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56 >seq1
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57 ACG
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58 >seq2
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59 TGTCATGAGAAAGACAGCCGACACTCAAGTCAACGTATCTCTGGT
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60
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61 -----
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62
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63 **ABI SOLiD Color Coding Alignment matrix**
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64
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65 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).
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66
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67
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68 .. image:: ./static/images/dualcolorcode.png
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69
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70
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71 </help>
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72 </tool>
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