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1 <tool id="fastqsolexa_to_fasta_qual" name="FASTQSOLEXA-to-FASTA-QUAL" version="1.0.0">
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2 <description>extracts sequences and quality scores from FASTQSOLEXA data</description>
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3 <command interpreter="python">fastqsolexa_to_fasta_qual.py $input1 $output1 $output2 $input1.extension</command>
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4 <inputs>
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5 <param name="input1" type="data" format="fastqsolexa" label="Fastqsolexa file"/>
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6 </inputs>
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7 <outputs>
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8 <data name="output1" format="fasta"/>
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9 <data name="output2" format="qualsolexa"/>
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10 </outputs>
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11 <tests>
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12 <!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
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13 <test>
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14 <param name="input1" value="1.fastqsolexa" ftype="fastqsolexa" />
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15 <output name="output1" file="fastqsolexa_to_fasta_qual_out4.fasta" />
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16 </test>
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17 <test>
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18 <param name="input1" value="2.fastqsolexa" ftype="fastqsolexa" />
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19 <output name="output1" file="fastqsolexa_to_fasta_qual_out2.fasta" />
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20 </test>
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21 </tests>
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22 <help>
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23
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24 .. class:: warningmark
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25
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26 IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64.
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27
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28 -----
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29
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30 **What it does**
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31
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32 This tool extracts sequences and quality scores from FASTQ data ( Solexa variant ), producing a FASTA dataset and a QUAL dataset.
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33
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34 -----
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35
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36 **Example1**
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37
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38 - Converting the following Solexa fastq data::
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39
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40 @seq1
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41 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
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42 +seq1
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43 hhhhhhhhhhhhhhhhhhhhhhhhhhPW@hhhhhh
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44 @seq2
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45 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
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46 +seq2
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47 hhhhhhhhhhhhhhYhhahhhhWhAhFhSIJGChO
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48
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49 - will extract the following sequences::
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50
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51 >seq1
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52 GACAGCTTGGTTTTTAGTGAGTTGTTCCTTTCTTT
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53 >seq2
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54 GCAATGACGGCAGCAATAAACTCAACAGGTGCTGG
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55
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56 - and quality scores::
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57
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58 >seq1
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59 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 40 16 23 0 40 40 40 40 40 40
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60 >seq2
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61 40 40 40 40 40 40 40 40 40 40 40 40 40 40 25 40 40 33 40 40 40 40 23 40 1 40 6 40 19 9 10 7 3 40 15
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62
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63 **Example2**
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64
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65 - Converting the following Solexa fastq data::
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66
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67 @HANNIBAL_1_FC302VTAAXX:2:1:228:167
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68 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
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69 +HANNIBAL_1_FC302VTAAXX:2:1:228:167
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70 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
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71 @HANNIBAL_1_FC302VTAAXX:2:1:156:340
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72 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
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73 +HANNIBAL_1_FC302VTAAXX:2:1:156:340
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74 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
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75
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76 - will extract the following sequences::
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77
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78 >HANNIBAL_1_FC302VTAAXX:2:1:228:167
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79 GAATTGATCAGGACATAGGACAACTGTAGGCACCAT
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80 >HANNIBAL_1_FC302VTAAXX:2:1:156:340
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81 GAGTTCTCGTCGCCTGTAGGCACCATCAATCGTATG
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82
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83 - and quality scores::
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84
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85 >HANNIBAL_1_FC302VTAAXX:2:1:228:167
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86 40 40 40 40 35 40 40 40 25 40 40 26 40 9 33 11 40 35 17 40 40 33 40 7 9 15 3 22 15 30 11 17 9 4 9 4
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87 >HANNIBAL_1_FC302VTAAXX:2:1:156:340
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88 40 15 40 17 6 36 40 40 40 25 40 9 35 33 40 14 14 18 15 17 19 28 31 4 24 18 27 14 15 18 2 8 12 8 11 9
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89
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90 </help>
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91 </tool>
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