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comparison bamCoverage.xml @ 27:bf1b1dcdd67b draft

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author bgruening
date Mon, 17 Mar 2014 16:23:58 -0400
parents 2ad3b027dfcd
children f7712a057440
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26:2ad3b027dfcd 27:bf1b1dcdd67b
1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.4"> 1 <tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.5">
2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description> 2 <description> generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <expand macro="stdio" /> 4 <expand macro="stdio" />
5 <macros> 5 <macros>
6 <token name="@BINARY@">bamCoverage</token> 6 <token name="@BINARY@">bamCoverage</token>
58 <param name="bamInput" format="bam" type="data" label="BAM file" 58 <param name="bamInput" format="bam" type="data" label="BAM file"
59 help="The BAM file must be sorted."/> 59 help="The BAM file must be sorted."/>
60 60
61 <param name="fragmentLength" type="integer" value="300" min="1" 61 <param name="fragmentLength" type="integer" value="300" min="1"
62 label="Length of the average fragment size" 62 label="Length of the average fragment size"
63 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/> 63 help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
64 64
65 <param name="binSize" type="integer" value="50" min="1" 65 <param name="binSize" type="integer" value="50" min="1"
66 label="Bin size in bp" 66 label="Bin size in bp"
67 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/> 67 help="The genome will be divided in bins (also called tiles) of the specified length. For each bin the overlaping number of fragments (or reads) will be reported. If only half a fragment overlaps, this fraction will be reported. "/>
68 68