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64 lines
1.7 KiB
XML
64 lines
1.7 KiB
XML
<tool id="cshl_fastx_reverse_complement" name="Reverse-Complement">
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<description></description>
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<requirements><requirement type="package">fastx_toolkit</requirement></requirements>
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<command>zcat -f '$input' | fastx_reverse_complement -v -o $output
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#if $input.ext == "fastqsanger":
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-Q 33
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#end if
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</command>
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<inputs>
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<param format="fasta,fastqsolexa,fastqsanger" name="input" type="data" label="Library to reverse-complement" />
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</inputs>
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<tests>
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<test>
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<!-- Reverse-complement a FASTA file -->
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<param name="input" value="fastx_rev_comp1.fasta" />
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<output name="output" file="fastx_reverse_complement1.out" />
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</test>
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<test>
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<!-- Reverse-complement a FASTQ file -->
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<param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/>
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<output name="output" file="fastx_reverse_complement2.out" />
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</test>
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</tests>
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<outputs>
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<data format="input" name="output" metadata_source="input" />
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</outputs>
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<help>
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**What it does**
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This tool reverse-complements each sequence in a library.
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If the library is a FASTQ, the quality-scores are also reversed.
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--------
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**Example**
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Input FASTQ file::
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@CSHL_1_FC42AGWWWXX:8:1:3:740
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TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA
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+CSHL_1_FC42AGWWWXX:8:1:3:740
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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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Output FASTQ file::
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@CSHL_1_FC42AGWWWXX:8:1:3:740
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TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA
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+CSHL_1_FC42AGWWWXX:8:1:3:740
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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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------
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This tool is based on `FASTX-toolkit`__ by Assaf Gordon.
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.. __: http://hannonlab.cshl.edu/fastx_toolkit/
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</help>
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</tool>
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