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comparison bamToBed.xml @ 0:b8348686a0b9 draft

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author iuc
date Tue, 04 Nov 2014 01:45:04 -0500
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children 82aac94b06c3
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-1:000000000000 0:b8348686a0b9
1 <tool id="bedtools_bamtobed" name="Convert from BAM to BED" 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 bamtobed
10 $option
11 $ed_score
12 -i '$input'
13 &gt; '$output'
14 #if str($tag):
15 -tag $tag
16 #end if
17 </command>
18 <inputs>
19 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
20 <param name="option" type="select" label="What type of BED output would you like">
21 <option value="">Create a 6-column BED file.</option>
22 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
23 <option value="-bedpe">Create a paired-end, BEDPE format.</option>
24 </param>
25 <param name="split" type="boolean" label="Report each portion of a split BAM alignment" truevalue="-split" falsevalue="" checked="false" help="(i.e., having an 'N' CIGAR operation) as a distinct BED intervals."/>
26 <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
27 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
28 </inputs>
29 <outputs>
30 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
31 </outputs>
32 <help>
33
34 **What it does**
35
36 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
37
38 .. class:: infomark
39
40 The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries. For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp. However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation). This is important for RNA-seq and structural variation experiments.
41
42
43 .. class:: warningmark
44
45 If using a custom BAM alignment TAG as the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
46
47 .. class:: warningmark
48
49 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
50
51 @REFERENCES@
52
53 </help>
54 <expand macro="citations" />
55 </tool>