[2] | 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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