Mercurial > repos > iuc > bedtools
view bamToFastq.xml @ 0:b8348686a0b9 draft
Imported from capsule None
author | iuc |
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date | Tue, 04 Nov 2014 01:45:04 -0500 |
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<tool id="bedtools_bamtofastq" name="Convert from BAM to FastQ" version="@WRAPPER_VERSION@.0"> <description></description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command> bedtools bamtofastq $tags $fq2 -i '$input' -fq '$output' </command> <inputs> <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/> <param name="tags" type="boolean" truevalue="-tags" falsevalue="" selected="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/> <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" selected="False" label="ASTQ for second end. Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/> </inputs> <outputs> <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/> </outputs> <help> **What it does** bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format. @REFERENCES@ </help> <expand macro="citations" /> </tool>