[2] | 1 | <tool id="split_paired_reads" name="Split paired end reads" version="1.0.0"> |
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| 2 | <description></description> |
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| 3 | <command interpreter="python"> |
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| 4 | split_paired_reads.py $input $output1 $output2 |
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| 5 | </command> |
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| 6 | <inputs> |
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| 7 | <param name="input" type="data" format="fastqsanger" label="Your paired-end file" /> |
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| 8 | </inputs> |
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| 9 | <outputs> |
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| 10 | <data name="output1" format="fastqsanger"/> |
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| 11 | <data name="output2" format="fastqsanger"/> |
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| 12 | </outputs> |
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| 13 | <tests> |
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| 14 | <test> |
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| 15 | <param name="input" value="3.fastqsanger" ftype="fastqsanger"/> |
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| 16 | <output name="output1" file="split_pair_reads_1.fastqsanger" ftype="fastqsanger"/> |
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| 17 | <output name="output2" file="split_pair_reads_2.fastqsanger" ftype="fastqsanger"/> |
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| 18 | </test> |
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| 19 | </tests> |
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| 20 | <help> |
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| 21 | |
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| 22 | **What it does** |
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| 23 | |
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| 24 | Splits a single fastq dataset representing paired-end run into two datasets (one for each end). This tool works only for datasets where both ends have **the same** length. |
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| 25 | |
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| 26 | ----- |
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| 27 | |
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| 28 | **Input formats** |
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| 29 | |
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| 30 | A multiple-fastq file, for example:: |
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| 31 | |
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| 32 | @HWI-EAS91_1_30788AAXX:7:21:1542:1758 |
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| 33 | GTCAATTGTACTGGTCAATACTAAAAGAATAGGATCGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA |
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| 34 | +HWI-EAS91_1_30788AAXX:7:21:1542:1758 |
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| 35 | hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR |
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| 36 | |
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| 37 | |
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| 38 | ----- |
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| 39 | |
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| 40 | **Outputs** |
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| 41 | |
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| 42 | One end:: |
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| 43 | |
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| 44 | @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 |
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| 45 | GTCAATTGTACTGGTCAATACTAAAAGAATAGGATC |
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| 46 | +HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 |
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| 47 | hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh |
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| 48 | |
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| 49 | The other end:: |
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| 50 | |
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| 51 | @HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 |
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| 52 | GCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCA |
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| 53 | +HWI-EAS91_1_30788AAXX:7:21:1542:1758/2 |
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| 54 | hhhhhhhhhhhhhhhhhhhhhhhh`hfhhVZSWehR |
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| 55 | |
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| 56 | </help> |
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| 57 | </tool> |
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