|
1
|
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 <![CDATA[
|
|
|
10 bedtools bedtobam
|
|
|
11 $bed12
|
|
|
12 -mapq $mapq
|
|
|
13 -g $genome
|
|
|
14 -i '$input'
|
|
|
15 > '$output'
|
|
|
16 ]]>
|
|
|
17 </command>
|
|
|
18 <inputs>
|
|
|
19 <param format="bed" name="input" type="data" label="Convert the following BED file to BAM"/>
|
|
|
20 <param name="bed12" type="boolean" truevalue="-bed12" falsevalue="" checked="false"
|
|
|
21 label="Indicate that the input BED file is in BED12 (a.k.a 'blocked' BED) format"
|
|
|
22 help="If Selected, bedToBam will convert blocked BED features (e.g., gene annotaions) into 'spliced' BAM alignments by creating an appropriate CIGAR string. (-bed12)"/>
|
|
|
23 <expand macro="genome" />
|
|
|
24 <param name="mapq" type="integer" value="255"
|
|
|
25 label="Set a mapping quality (SAM MAPQ field) value for all BED entries" help="(-mapq)"/>
|
|
|
26 </inputs>
|
|
|
27 <outputs>
|
|
|
28 <data format="bam" name="output" metadata_source="input" label="${input.name} (as BAM)"/>
|
|
|
29 </outputs>
|
|
|
30 <tests>
|
|
|
31 <test>
|
|
|
32 <param name="input" value="bedToBam1.bed" ftype="bed" />
|
|
|
33 <param name="genome" value="mm9_chr1.len" ftype="tabular" />
|
|
|
34 <output name="output" file="bedToBam_result.bam" lines_diff="2" ftype="bam" />
|
|
|
35 </test>
|
|
|
36 </tests>
|
|
|
37 <help>
|
|
|
38 <![CDATA[
|
|
|
39 **What it does**
|
|
|
40
|
|
|
41 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.
|
|
|
42
|
|
|
43 @REFERENCES@
|
|
|
44 ]]>
|
|
|
45 </help>
|
|
|
46 <expand macro="citations" />
|
|
|
47 </tool>
|
