Mercurial > repos > iuc > bedtools
diff bedpeToBam.xml @ 0:b8348686a0b9 draft
Imported from capsule None
author | iuc |
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date | Tue, 04 Nov 2014 01:45:04 -0500 |
parents | |
children | 82aac94b06c3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedpeToBam.xml Tue Nov 04 01:45:04 2014 -0500 @@ -0,0 +1,38 @@ +<tool id="bedtools_bedpetobam" name="Convert from BEDPE to BAM" version="@WRAPPER_VERSION@.0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command> + bedtools bedpetobam + $ubam + -mapq $mapq + -i '$input' + -g $genome + > '$output' + </command> + <inputs> + <param format="bed,gff,vcf" name="input" type="data" label="BED/VCF/GFF file"/> + <expand macro="genome" /> + <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" /> + <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/> + </inputs> + <outputs> + <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> + </outputs> + <help> + +**What it does** + +Converts feature records to BAM format. + +.. class:: warningmark + +BED files must be at least BED4 to create BAM (needs name field). + +@REFERENCES@ + </help> + <expand macro="citations" /> +</tool>