Mercurial > repos > nikos > bigwig_to_wig
changeset 4:84f9377544ad draft
Uploaded
| author | nikos |
|---|---|
| date | Wed, 30 Jul 2014 10:35:20 -0400 |
| parents | 52f48427f2a4 |
| children | 4f227ae81c46 |
| files | bigwig_to_wig.xml |
| diffstat | 1 files changed, 32 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bigwig_to_wig.xml Wed Jul 30 10:35:20 2014 -0400 @@ -0,0 +1,32 @@ +<tool id="bigwig_to_wig" name="BigWig to Wig" version="1.0.0"> + <description>converter</description> + <command>/home/jens/bin/bigwig2wig_stdout -f $input -b $bin_size -l $mylab > $output + </command> + <requirements> + <requirement type="package">bigWigSummary</requirement> + <requirement type="package">bigwig2wig</requirement> + <requirement type="package">bigWigInfo</requirement> + </requirements> + <inputs> + <param format="bigwig" name="input" type="data" label="BigWig file to convert"> + </param> + <param name="bin_size" size="4" type="integer" value="500" label="Bin size" help="Must be an even integer > 100." /> + <param name="mylab" type="text" value="wiggle_file" label="Output file prefix" help="" /> + </inputs> + <outputs> + <data format="wig" name="output" label="${mylab}_density_bin${bin_size}.wig" /> + </outputs> + <tests> + </tests> + <help> + +This tool converts a **BigWig** file to fixed step **Wiggle** format. +Resolution is controlled through the bin size (the higher the size, the lower the resolution). + +The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigInfo_ and bigWigSummary_. + +.. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo +.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary + +</help> +</tool>