Mercurial > repos > nikos > bigwig_to_wig
changeset 1:8eaf0cc6a54f draft
Uploaded
| author | nikos |
|---|---|
| date | Wed, 30 Jul 2014 10:32:46 -0400 |
| parents | 3e0b7c446e7f |
| children | 049625551a0f |
| files | bigwig_to_wig.xml |
| diffstat | 1 files changed, 576 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 10:32:46 2014 -0400 @@ -0,0 +1,576 @@ + + + + + +<!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" 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rel="author">sidiropoulos</a></span> + <time datetime="2014-07-30T14:52:25+02:00" is="relative-time">July 30, 2014</time> + <div class="commit-title"> + <a href="/sidiropoulos/galaxytools/commit/03ed1f1103f350fd4ab2b420252ae9245ffd7808" class="message" data-pjax="true" title="bigWig to Wig converter.">bigWig to Wig converter.</a> + </div> + + <div class="participation"> + <p class="quickstat"><a href="#blob_contributors_box" rel="facebox"><strong>1</strong> contributor</a></p> + + </div> + <div id="blob_contributors_box" style="display:none"> + <h2 class="facebox-header">Users who have contributed to this file</h2> + <ul class="facebox-user-list"> + <li class="facebox-user-list-item"> + <img alt="sidiropoulos" data-user="8235731" height="24" src="https://avatars0.githubusercontent.com/u/8235731?v=1&s=48" width="24" /> + <a href="/sidiropoulos">sidiropoulos</a> + </li> + </ul> + </div> + </div> + +<div class="file-box"> + <div class="file"> + <div class="meta clearfix"> + <div class="info file-name"> + <span>33 lines (28 sloc)</span> + <span class="meta-divider"></span> + <span>1.377 kb</span> + </div> + <div class="actions"> + <div class="button-group"> + <a href="/sidiropoulos/galaxytools/raw/master/bigwig_to_wig/bigwig_to_wig.xml" class="minibutton " id="raw-url">Raw</a> + <a href="/sidiropoulos/galaxytools/blame/master/bigwig_to_wig/bigwig_to_wig.xml" class="minibutton js-update-url-with-hash">Blame</a> + <a href="/sidiropoulos/galaxytools/commits/master/bigwig_to_wig/bigwig_to_wig.xml" class="minibutton " rel="nofollow">History</a> + </div><!-- /.button-group --> + + + <a class="octicon-button disabled tooltipped tooltipped-w" href="#" + aria-label="You must be signed in to make or propose changes"><span class="octicon octicon-pencil"></span></a> + + <a class="octicon-button danger disabled tooltipped tooltipped-w" href="#" + aria-label="You must be signed in to make or propose changes"> + <span class="octicon octicon-trashcan"></span> + </a> + </div><!-- /.actions --> + </div> + + <div class="blob-wrapper data type-xml"> + <table class="file-code file-diff tab-size-8"> + <tr class="file-code-line"> + <td class="blob-line-nums"> + <span id="L1" rel="#L1">1</span> +<span id="L2" rel="#L2">2</span> +<span id="L3" rel="#L3">3</span> +<span id="L4" rel="#L4">4</span> +<span id="L5" rel="#L5">5</span> +<span id="L6" rel="#L6">6</span> +<span id="L7" rel="#L7">7</span> +<span id="L8" rel="#L8">8</span> +<span id="L9" rel="#L9">9</span> +<span id="L10" rel="#L10">10</span> +<span id="L11" rel="#L11">11</span> +<span id="L12" rel="#L12">12</span> +<span id="L13" rel="#L13">13</span> +<span id="L14" rel="#L14">14</span> +<span id="L15" rel="#L15">15</span> +<span id="L16" rel="#L16">16</span> +<span id="L17" rel="#L17">17</span> +<span id="L18" rel="#L18">18</span> +<span id="L19" rel="#L19">19</span> +<span id="L20" rel="#L20">20</span> +<span id="L21" rel="#L21">21</span> +<span id="L22" rel="#L22">22</span> +<span id="L23" rel="#L23">23</span> +<span id="L24" rel="#L24">24</span> +<span id="L25" rel="#L25">25</span> +<span id="L26" rel="#L26">26</span> +<span id="L27" rel="#L27">27</span> +<span id="L28" rel="#L28">28</span> +<span id="L29" rel="#L29">29</span> +<span id="L30" rel="#L30">30</span> +<span id="L31" rel="#L31">31</span> +<span id="L32" rel="#L32">32</span> + + </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> + </tr> + </table> + </div> + + </div> +</div> + +<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" 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