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comparison galaxy-conf/MapDyads.xml @ 12:81d5b81fb3c2 draft

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Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
author timpalpant
date Wed, 25 Apr 2012 16:53:48 -0400
parents b1952a90d4bf
children 3e477c7e0e73
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11:b1952a90d4bf 12:81d5b81fb3c2
24 <outputs> 24 <outputs>
25 <data name="output" format="wig" /> 25 <data name="output" format="wig" />
26 </outputs> 26 </outputs>
27 27
28 <help> 28 <help>
29
30 This tool produces a Wig file with the number of dyads at each base pair. For paired-end MNase data, dyads are approximated using the center of the fragment. For Bed/BedGraph formatted input, this means the center of the interval; for SAM/BAM formatted input, this means the middle between the 5' end of mate 1 and the 5' end of mate 2. For single-end data, the estimated mononucleosome fragment length (N) must be specified, which will be used to offset reads from the + and - strands by +/- N/2.
31
29 .. class:: warningmark 32 .. class:: warningmark
30 33
31 This tool requires sequencing reads in SAM, BAM, Bed format. 34 This tool requires sequencing reads in SAM, BAM, Bed, or BedGraph format.
32 35
33 .. class:: warningmark 36 .. class:: warningmark
34 37
35 For paired-end MNase data, read centers are approximated using the center of the read. For single-end data, the estimated mononucleosome fragment length must be specified, which will be used to offset reads from the + and - strands. 38 Since BedGraph format does not contain strand information, all reads in BedGraph format are considered to be on the 5' strand.
39
36 </help> 40 </help>
37 </tool> 41 </tool>