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comparison multiCov.xml @ 0:b8348686a0b9 draft

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Imported from capsule None
author iuc
date Tue, 04 Nov 2014 01:45:04 -0500
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1 <tool id="bedtools_multicovtbed" name="MultiCovBed" 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 multicov
10 -bed $input1
11 -bam
12 #for $bam in $bams:
13 $bam.input
14 #end for
15 $strand
16 -f $overlap
17 $reciprocal
18 $split
19 -q $mapq
20 $duplicate
21 $failed
22 $proper
23 &gt; $output
24 </command>
25 <inputs>
26 <param name="input1" format="bed" type="data" label="First sorted BED file" />
27 <!-- Additional files, if the user needs more -->
28 <repeat name="bams" title="Add BAM files" >
29 <param name="input" format="bam" type="data" label="BAM file" />
30 </repeat>
31 <expand macro="strand2" />
32 <expand macro="overlap" />
33 <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Require that the fraction overlap be reciprocal for A and B. In other words, if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B." />
34 <expand macro="split" />
35
36 <param name="duplicate" type="boolean" checked="false" truevalue="-D" falsevalue="" label="Include duplicate reads. Default counts non-duplicates only" />
37 <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue="" label=" Include failed-QC reads. Default counts pass-QC reads only" />
38 <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Only count proper pairs. Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field." />
39 </inputs>
40
41 <outputs>
42 <data format="bed" name="output" label="" />
43 </outputs>
44 <help>
45
46 **What it does**
47
48 bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
49
50 .. class:: infomark
51
52 bedtools multicov depends upon index BAM files in order to count the number of overlaps in each BAM file. As such, each BAM file should be position sorted (samtool sort aln.bam aln.sort) and indexed (samtools index aln.sort.bam) with either samtools or bamtools.
53
54 @REFERENCES@
55
56 </help>
57 <expand macro="citations" />
58 </tool>