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comparison BedToBam.xml @ 0:4fb5ea02b441 draft

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author iuc
date Tue, 15 Jul 2014 14:42:23 -0400
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1 <tool id="bedtools_bedtobam" name="Convert from BED to BAM" version="@WRAPPER_VERSION@.0">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="stdio" />
8 <command>
9 bedtools bedtobam
10 $ubam
11 $bed12
12 -mapq $mapq
13 -i '$input'
14 &gt; '$output'
15 </command>
16 <inputs>
17 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
18 <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/>
19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" />
20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/>
21 </inputs>
22 <outputs>
23 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
24 </outputs>
25 <help>
26
27 **What it does**
28
29 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.
30
31 @REFERENCES@
32 </help>
33 </tool>