Mercurial > repos > iuc > bedtools
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamToFastq.xml Tue Nov 04 01:45:04 2014 -0500 @@ -0,0 +1,33 @@ +<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>