Mercurial > repos > devteam > fastx_reverse_complement
view fastx_reverse_complement.xml @ 4:64203edc4ec1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_reverse_complement commit 3953b65f6b1c0336e9cadbe0792a5d3b14b5643a
author | iuc |
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date | Wed, 22 Aug 2018 11:03:42 -0400 |
parents | 9d06c848a628 |
children | a4167b7c73cb |
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<tool id="cshl_fastx_reverse_complement" version="1.0.2" name="Reverse-Complement"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @CATS@ fastx_reverse_complement -v -o '$output' @FQQUAL@ @GZIP@ ]]></command> <inputs> <expand macro="fastx_input" /> </inputs> <outputs> <data name="output" format_source="input" metadata_source="input" /> </outputs> <tests> <test> <!-- Reverse-complement a FASTA file --> <param name="input" value="fastx_rev_comp1.fasta" /> <output name="output" ftype="fasta" file="fastx_reverse_complement1.out" /> </test> <test> <!-- Reverse-complement a FASTQ file --> <param name="input" value="fastx_rev_comp2.fastq" ftype="fastqsolexa"/> <output name="output" ftype="fastqsolexa" file="fastx_reverse_complement2.out" /> </test> </tests> <help><![CDATA[ **What it does** This tool reverse-complements each sequence in a library. If the library is a FASTQ, the quality-scores are also reversed. -------- **Example** Input FASTQ file:: @CSHL_1_FC42AGWWWXX:8:1:3:740 TGTCTGTAGCCTCNTCCTTGTAATTCAAAGNNGGTA +CSHL_1_FC42AGWWWXX:8:1:3:740 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 Output FASTQ file:: @CSHL_1_FC42AGWWWXX:8:1:3:740 TACCNNCTTTGAATTACAAGGANGAGGCTACAGACA +CSHL_1_FC42AGWWWXX:8:1:3:740 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 ------ This tool is based on `FASTX-toolkit`__ by Assaf Gordon. .. __: http://hannonlab.cshl.edu/fastx_toolkit/ ]]></help> <expand macro="citations" /> </tool>