Mercurial > repos > nikos > bigwig_to_wig
changeset 3:52f48427f2a4 draft
Deleted selected files
| author | nikos |
|---|---|
| date | Wed, 30 Jul 2014 10:34:47 -0400 |
| parents | 049625551a0f |
| children | 84f9377544ad |
| files | bigwig_to_wig.xml |
| diffstat | 1 files changed, 0 insertions(+), 576 deletions(-) [+] |
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--- a/bigwig_to_wig.xml Wed Jul 30 10:33:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,576 +0,0 @@ - - - - - -<!DOCTYPE html> -<html class=" "> - <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#"> - <meta charset='utf-8'> - <meta http-equiv="X-UA-Compatible" content="IE=edge"> - - - <title>galaxytools/bigwig_to_wig/bigwig_to_wig.xml at master · sidiropoulos/galaxytools · GitHub</title> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> - <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png"> - <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144.png"> - 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- </td> - <td class="blob-line-code"><div class="code-body highlight"><pre><div class='line' id='LC1'><span class="nt"><tool</span> <span class="na">id=</span><span class="s">"bigwig_to_wig"</span> <span class="na">name=</span><span class="s">"BigWig to Wig"</span> <span class="na">version=</span><span class="s">"1.0.0"</span><span class="nt">></span></div><div class='line' id='LC2'> <span class="nt"><description></span>converter<span class="nt"></description></span></div><div class='line' id='LC3'> <span class="nt"><command></span>/home/jens/bin/bigwig2wig_stdout -f $input -b $bin_size -l $mylab > $output </div><div class='line' id='LC4'> <span class="nt"></command></span></div><div class='line' id='LC5'> <span class="nt"><requirements></span></div><div class='line' id='LC6'> <span class="nt"><requirement</span> <span class="na">type=</span><span class="s">"package"</span><span class="nt">></span>bigWigSummary<span class="nt"></requirement></span></div><div class='line' id='LC7'> <span class="nt"><requirement</span> <span class="na">type=</span><span class="s">"package"</span><span class="nt">></span>bigwig2wig<span class="nt"></requirement></span></div><div class='line' id='LC8'> <span class="nt"><requirement</span> <span class="na">type=</span><span class="s">"package"</span><span class="nt">></span>bigWigInfo<span class="nt"></requirement></span></div><div class='line' id='LC9'> <span class="nt"></requirements></span></div><div class='line' id='LC10'> <span class="nt"><inputs></span></div><div class='line' id='LC11'> <span class="nt"><param</span> <span class="na">format=</span><span class="s">"bigwig"</span> <span class="na">name=</span><span class="s">"input"</span> <span class="na">type=</span><span class="s">"data"</span> <span class="na">label=</span><span class="s">"BigWig file to convert"</span><span class="nt">></span></div><div class='line' id='LC12'> <span class="nt"></param></span></div><div class='line' id='LC13'> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"bin_size"</span> <span class="na">size=</span><span class="s">"4"</span> <span class="na">type=</span><span class="s">"integer"</span> <span class="na">value=</span><span class="s">"500"</span> <span class="na">label=</span><span class="s">"Bin size"</span> <span class="na">help=</span><span class="s">"Must be an even integer > 100."</span> <span class="nt">/></span></div><div class='line' id='LC14'> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"mylab"</span> <span class="na">type=</span><span class="s">"text"</span> <span class="na">value=</span><span class="s">"wiggle_file"</span> <span class="na">label=</span><span class="s">"Output file prefix"</span> <span class="na">help=</span><span class="s">""</span> <span class="nt">/></span></div><div class='line' id='LC15'> <span class="nt"></inputs></span></div><div class='line' id='LC16'> <span class="nt"><outputs></span></div><div class='line' id='LC17'> <span class="nt"><data</span> <span class="na">format=</span><span class="s">"wig"</span> <span class="na">name=</span><span class="s">"output"</span> <span class="na">label=</span><span class="s">"${mylab}_density_bin${bin_size}.wig"</span> <span class="nt">/></span></div><div class='line' id='LC18'> <span class="nt"></outputs></span></div><div class='line' id='LC19'> <span class="nt"><tests></span></div><div class='line' id='LC20'> <span class="nt"></tests></span></div><div class='line' id='LC21'> <span class="nt"><help></span></div><div class='line' id='LC22'><br></div><div class='line' id='LC23'>This tool converts a **BigWig** file to fixed step **Wiggle** format. </div><div class='line' id='LC24'>Resolution is controlled through the bin size (the higher the size, the lower the resolution).</div><div class='line' id='LC25'><br></div><div class='line' id='LC26'>The script this tool is based on is written by Jens Vilstrup Johansen and uses bigWigInfo_ and bigWigSummary_.</div><div class='line' id='LC27'><br></div><div class='line' id='LC28'>.. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo</div><div class='line' id='LC29'>.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary</div><div class='line' id='LC30'><br></div><div class='line' id='LC31'><span class="nt"></help></span></div><div class='line' id='LC32'><span class="nt"></tool></span></div></pre></div></td> - 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