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comparison bamCoverage.xml @ 9:c53a73b8eef9 draft

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Uploaded
author bgruening
date Tue, 10 Dec 2013 12:13:18 -0500
parents d957e25e18a3
children 135f3bae5c56
comparison
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8:1c5ed9126db6 9:c53a73b8eef9
46 46
47 #end if 47 #end if
48 </command> 48 </command>
49 49
50 <inputs> 50 <inputs>
51 <param name="bamInput" format="bam" type="data" label="Input BAM file" 51 <param name="bamInput" format="bam" type="data" label="BAM file"
52 help="The BAM file must be sorted."/> 52 help="The BAM file must be sorted."/>
53 53
54 <param name="fragmentLength" type="integer" value="300" min="1" 54 <param name="fragmentLength" type="integer" value="300" min="1"
55 label="Length of the average fragment size" 55 label="Length of the average fragment size"
56 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."/> 56 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."/>