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comparison multiCov.xml @ 8:0d3aa592ce27 draft

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author iuc
date Tue, 28 Apr 2015 22:56:34 -0400
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7:76db45de75c6 8:0d3aa592ce27
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 <![CDATA[
10 #for $i, $bam in enumerate( $bams ):
11 ln -s -f $bam ${i}.bam &&
12 ln -s -f $bam.metadata.bam_index ${i}.bam.bai &&
13 #end for
14
15 bedtools multicov
16 -bed $input
17 -bams
18 #for $i, $bam in enumerate( $bams ):
19 ${i}.bam
20 #end for
21 $strand
22 -f $overlap
23 $reciprocal
24 $split
25 -q $q
26 $duplicate
27 $failed
28 $proper
29 > $output
30 ]]>
31 </command>
32 <inputs>
33 <param name="input" format="bed" type="data" label="Sorted BED file" />
34 <!-- Additional files, if the user needs more -->
35 <param name="bams" format="bam" type="data" multiple="True" label="BAM file" />
36
37 <expand macro="strand2" />
38 <expand macro="overlap" />
39 <expand macro="reciprocal" />
40 <expand macro="split" />
41 <param name="q" type="integer" value="0" label="Minimum mapping quality (MAPQ) allowed" help="(-q)" />
42 <param name="duplicate" type="boolean" checked="False" truevalue="-D" falsevalue=""
43 label="Include duplicate reads"
44 help="Default counts non-duplicates only. (-D)" />
45 <param name="failed" type="boolean" checked="false" truevalue="-F" falsevalue=""
46 label="Include failed-QC reads"
47 help="Default counts pass-QC reads only (-F)"/>
48 <param name="proper" type="boolean" checked="false" truevalue="-p" falsevalue=""
49 label="Only count proper pairs"
50 help="Default counts all alignments with MAPQ > -q argument, regardless of the BAM FLAG field. (-p)" />
51 </inputs>
52 <outputs>
53 <data name="output" metadata_source="input" format_source="input" />
54 </outputs>
55 <tests>
56 <test>
57 <param name="input" value="multiCov1.bed" ftype="bed" />
58 <param name="bams" value="srma_in3.bam,srma_in3.bam" ftpye="bam"/>
59 <param name="q" value="1"/>
60 <param name="split" value="False"/>
61 <output name="output" file="multiCovBed_result1.bed" ftype="bed" />
62 </test>
63 </tests>
64 <help>
65 <![CDATA[
66 **What it does**
67
68 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.
69
70
71 @REFERENCES@
72 ]]>
73 </help>
74 <expand macro="citations" />
75 </tool>