Mercurial > repos > nikos > ucsc_tools
changeset 3:e8301c182e8c draft
Uploaded
author | nikos |
---|---|
date | Tue, 15 Jul 2014 07:19:05 -0400 |
parents | e6502d9fe0dd |
children | 5b5460b79488 |
files | bigwig2summary.xml |
diffstat | 1 files changed, 85 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwig2summary.xml Tue Jul 15 07:19:05 2014 -0400 @@ -0,0 +1,85 @@ +<tool id="bigwig2_summary" name="bigWig2Summary"> + <description> Extract summary information from a bigWig file across multiple genomic regions specified by the user. </description> + <requirements> + <requirement type="package">bigWigSummary</requirement> + <requirement type="package">bigwig2summary_stdout</requirement> + <requirement type="package">bedClip</requirement> + </requirements> + <command> + /home/jens/bin/bigwig2summary_stdout -f $input_bw -b $input_bed -n $bins -o $assembly -t $type $header > $output + </command> + <inputs> + <param name="input_bw" type="data" format="bigwig" label="Extract summary from" help="bigWig format."/> + <param name="input_bed" type="data" format="tabular" label="using genomic regions in" help="TAB delimited BED-like file."/> + <param name="bins" type="integer" value="1" label="Number of bins" help="Postitive integer"/> + <param name="assembly" type="text" label="Orgamism assembly" help="E.g. hg19" /> + <param name="header" type="boolean" checked="False" truevalue="-e" falsevalue=" " label="Does the genomic region file contain a header?" /> + <param name="type" type="select" label="Operation" help=""> + <option value="mean">Average value in region (default)</option> + <option value="min">Minimum value in region</option> + <option value="max">Maximum value in region</option> + <option value="std">Standard deviation in region</option> + <option value="coverage">Percentage of region that is covered</option> + </param> + </inputs> + + <outputs> + <data format="tabular" name="output"/> + </outputs> + <help> + +This tool extracts summary values (mean, min, max, std or coverage) from a **bigWig** file for a number of equal sized bins across genomic regions given in an a "BED-like" file. + +The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigSummary_ and bedClip_. + +.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary + +.. _bedClip: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedClip + +----- + +.. class:: infomark + +The file contaning the genomic region must be TAB-delimited with at list 3 columns representing Chromosome, ChrStart and ChrEnd. If the file contains 6 columns (or more), column 6 is expected to contain strand information. Summary values from a negative strand will be reversed. + +----- + +**Example 1** + +Input BED file:: + + chr19 50178708 50180708 + chr6 90348174 90350174 + chr16 58495848 58497848 + chr5 180580242 180582242 + chr9 120177017 120179017 + +Extract summary (*#* of bins = 3):: + + 0 0 0 + 0.144886 0 0 + 0.507327 1.14649 1.38456 + 0.221471 0.144886 0.309857 + 0.348944 0.426638 0.244495 + +**Example 2** + +Input BED file (with strand information):: + + chr19 50178708 50180708 NM_198318 0 + PRMT1 + chr6 90348174 90350174 NM_020466 0 - LYRM2 + chr16 58495848 58497848 NM_020465 0 + NDRG4 + chr5 180580242 180582242 NM_206880 0 + OR2V2 + chr9 120177017 120179017 NM_014010 0 - ASTN2 + +Extract summary (*#* of bins = 3):: + + 0 0 0 + 0 0 0.144886 + 0.507327 1.14649 1.38456 + 0.221471 0.144886 0.309857 + 0.244495 0.426638 0.348944 + + </help> +</tool> +