Mercurial > repos > iuc > bedtools
comparison 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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-1:000000000000 | 0:b8348686a0b9 |
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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 > '$output' | |
15 </command> | |
16 <inputs> | |
17 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/> | |
18 <param name="bed12" type="boolean" label="Indicate that the input BED file is in BED12 (a.k.a “blocked” BED) format" truevalue="-bed12" falsevalue="" checked="false" help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into “spliced” BAM alignments by creating an appropriate CIGAR string.."/> | |
19 <param name="mapq" type="integer" label="Set a mapping quality (SAM MAPQ field) value for all BED entries" value="255" /> | |
20 <param name="ubam" type="boolean" label="Write uncompressed BAM output." truevalue="-ubam" falsevalue="" checked="false"/> | |
21 </inputs> | |
22 <outputs> | |
23 <data format="bam" name="output" metadata_source="input" label="${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 <expand macro="citations" /> | |
34 </tool> |