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comparison bamToBed.xml @ 10:71af3ebbbb7a draft

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author iuc
date Wed, 29 Apr 2015 12:06:53 -0400
parents 0d3aa592ce27
children a2d4c30ba2f9
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9:21f1d1c5467b 10:71af3ebbbb7a
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 <![CDATA[
10 bedtools bamtobed
11 $option
12 $ed_score
13 $split
14 #if $tag and str($tag).strip():
15 -tag "${tag}"
16 #end if
17 -i "${input}"
18 > "${output}"
19 ]]>
20 </command>
21 <inputs>
22 <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
23 <param name="option" type="select" label="What type of BED output would you like">
24 <option value="">Create a 6-column BED file.</option>
25 <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
26 <option value="-bedpe">Create a paired-end, BEDPE format.</option>
27 </param>
28 <expand macro="split" />
29 <param name="ed_score" type="boolean" truevalue="-ed" falsevalue="" checked="false"
30 label="Use alignment's edit-distance for BED score" />
31 <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"
32 help="(-tag)"/>
33 </inputs>
34 <outputs>
35 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
36 </outputs>
37 <tests>
38 <test>
39 <param name="input" value="srma_in3.bam" ftype="bam" />
40 <param name="option" value="" />
41 <param name="tag" value="" />
42 <output name="output" file="bamToBed_result1.bed" ftype="bed" />
43 </test>
44 <test>
45 <param name="input" value="srma_in3.bam" ftype="bam" />
46 <param name="option" value="" />
47 <param name="tag" value="NM" />
48 <output name="output" file="bamToBed_result2.bed" ftype="bed" />
49 </test>
50 </tests>
51 <help>
52 <![CDATA[
53 **What it does**
54
55 bedtools bamtobed is a conversion utility that converts sequence alignments in BAM format into BED, BED12, and/or BEDPE records.
56
57 .. class:: infomark
58
59 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.
60
61
62 .. class:: warningmark
63
64 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).
65
66 .. class:: warningmark
67
68 If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
69
70 @REFERENCES@
71 ]]>
72 </help>
73 <expand macro="citations" />
74 </tool>