Mercurial > repos > timpalpant > java_genomics_toolkit
view galaxy-conf/NRLCalculator.xml @ 14:f58706d4d421 draft
Uploaded
author | timpalpant |
---|---|
date | Sat, 19 May 2012 10:40:16 -0400 |
parents | 81d5b81fb3c2 |
children |
line wrap: on
line source
<tool id="NRLCalculator" name="Compute the NRL" version="1.0.0"> <description>from nucleosome calls</description> <command interpreter="sh">galaxyToolRunner.sh nucleosomes.NRLCalculator -i $input -l $windows -o $output</command> <inputs> <param format="tabular" name="input" type="data" label="Nucleosome calls" /> <param format="bed,bedgraph,gff" name="windows" type="data" label="List of intervals/genes" /> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> <help> 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. :: chr start stop id alignment strand +1-to-+2 +2-to-+3 ... Each interval will have a different number of columns based on the number of nucleosome calls that were in that interval. ----- .. class:: warningmark 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. .. class:: warningmark This tool requires a set of nucleosome calls as input in the format created by the Nucleosomes -> Call Nucleosomes tool. .. class:: warningmark Intervals must be provided in Bed, BedGraph, or GFF format. BedGraph intervals are always considered to be on the + strand. </help> </tool>