Mercurial > repos > iuc > bedtools
diff bamToFastq.xml @ 4:607c0576c6ab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
author | iuc |
---|---|
date | Wed, 27 Jan 2016 15:15:59 -0500 |
parents | |
children | c78cf6fe3018 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bamToFastq.xml Wed Jan 27 15:15:59 2016 -0500 @@ -0,0 +1,39 @@ +<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 + $tags + -i '$input' + -fq '$output' + #if $fq2: + -fq2 '$output2' + #end if + </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="FASTQ 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="${input.name} (as FASTQ)"/> + <data format="fastq2" name="output2" metadata_source="input" label="${input.name} (as FASTQ)"> + <filter>fq2 is True</filter> + </data> + </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>