Mercurial > repos > timpalpant > java_genomics_toolkit

annotate galaxy-conf/NRLCalculator.xml @ 14:f58706d4d421 draft

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author timpalpant
date Sat, 19 May 2012 10:40:16 -0400
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1 <tool id="NRLCalculator" name="Compute the NRL" version="1.0.0">
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2 <description>from nucleosome calls</description>
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3 <command interpreter="sh">galaxyToolRunner.sh nucleosomes.NRLCalculator -i $input -l $windows -o $output</command>
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4 <inputs>
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5 <param format="tabular" name="input" type="data" label="Nucleosome calls" />
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6 <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals/genes" />
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7 </inputs>
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8 <outputs>
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9 <data format="tabular" name="output" />
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10 </outputs>
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12 <help>
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14 This tool calculates the distance between adjacent nucleosome calls (dyads) emanating from the 5' end of an interval. For each interval, the distance is calculated from the +1 to +2 nucleosome, +2 to +3 nucleosome, etc. These distances are appended as additional columns for each interval. ::
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16 chr start stop id alignment strand +1-to-+2 +2-to-+3 ...
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18 Each interval will have a different number of columns based on the number of nucleosome calls that were in that interval.
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20 -----
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22 .. class:: warningmark
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24 Because the distances are calculated from the 5' end of each gene, as you move into the gene body it becomes more likely that a nucleosome call will be skipped, resulting in an outlier distance (~320bp rather than ~165bp). In addition, nucleosome calls in fuzzy regions tend to be inaccurate, so the NRL distances will not be robust.
81d5b81fb3c2 Added help for all tools in the toolkit. Many bug fixes and a few new nucleosome tools.
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26 .. class:: warningmark
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28 This tool requires a set of nucleosome calls as input in the format created by the Nucleosomes -> Call Nucleosomes tool.
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30 .. class:: warningmark
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32 Intervals must be provided in Bed, BedGraph, or GFF format. BedGraph intervals are always considered to be on the + strand.
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34 </help>
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35 </tool>