Mercurial > repos > iuc > bedtools
diff BedToBam.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/BedToBam.xml Tue Nov 04 01:45:04 2014 -0500 @@ -0,0 +1,34 @@ +<tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <command> + bedtools bedtobam + $ubam + $bed12 + -mapq $mapq + -i '$input' + > '$output' + </command> + <inputs> + <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> + <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/> + <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" /> + <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/> + </inputs> + <outputs> + <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/> + </outputs> + <help> + +**What it does** + +bedToBam converts features in a feature file to BAM format. This is useful as an efficient means of storing large genome annotations in a compact, indexed format for visualization purposes. + +@REFERENCES@ + </help> + <expand macro="citations" /> +</tool>