[2] | 1 | <tool id="cshl_fastx_reverse_complement" name="Reverse-Complement"> |
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| 2 | <description></description> |
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| 3 | <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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| 4 | <command>zcat -f '$input' | fastx_reverse_complement -v -o $output</command> |
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| 5 | <inputs> |
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| 6 | <param format="fasta,fastqsolexa" name="input" type="data" label="Library to reverse-complement" /> |
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| 7 | </inputs> |
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| 8 | |
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| 9 | <tests> |
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| 10 | <test> |
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| 11 | <!-- Reverse-complement a FASTA file --> |
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| 12 | <param name="input" value="fastx_rev_comp1.fasta" /> |
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| 13 | <output name="output" file="fastx_reverse_complement1.out" /> |
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| 14 | </test> |
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| 15 | <test> |
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| 16 | <!-- Reverse-complement a FASTQ file --> |
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| 17 | <param name="input" value="fastx_rev_comp2.fastq" /> |
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| 18 | <output name="output" file="fastx_reverse_complement2.out" /> |
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| 19 | </test> |
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| 20 | </tests> |
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| 21 | |
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| 22 | |
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| 23 | <outputs> |
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| 24 | <data format="input" name="output" metadata_source="input" /> |
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| 25 | </outputs> |
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| 26 | |
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| 27 | <help> |
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| 28 | **What it does** |
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| 29 | |
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| 30 | This tool reverse-complements each sequence in a library. |
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| 31 | If the library is a FASTQ, the quality-scores are also reversed. |
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| 32 | |
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| 33 | -------- |
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| 34 | |
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| 35 | **Example** |
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| 36 | |
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| 37 | Input FASTQ file:: |
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| 38 | |
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| 39 | @CSHL_1_FC42AGWWWXX:8:1:3:740 |
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| 40 | TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA |
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| 41 | +CSHL_1_FC42AGWWWXX:8:1:3:740 |
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| 42 | 33 33 33 34 33 33 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 27 21 27 33 32 31 29 26 24 5 5 15 17 27 26 |
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| 43 | |
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| 44 | |
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| 45 | Output FASTQ file:: |
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| 46 | |
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| 47 | @CSHL_1_FC42AGWWWXX:8:1:3:740 |
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| 48 | TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA |
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| 49 | +CSHL_1_FC42AGWWWXX:8:1:3:740 |
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| 50 | 26 27 17 15 5 5 24 26 29 31 32 33 27 21 27 33 33 33 33 33 33 27 5 27 33 33 33 33 33 33 33 33 34 33 33 33 |
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| 51 | |
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| 52 | ------ |
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| 53 | |
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| 54 | This tool is based on `FASTX-toolkit`__ by Assaf Gordon. |
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| 55 | |
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| 56 | .. __: http://hannonlab.cshl.edu/fastx_toolkit/ |
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| 57 | |
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| 58 | </help> |
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| 59 | </tool> |
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