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
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+      <span class="author"><a href="/sidiropoulos" rel="author">sidiropoulos</a></span>
+      <time datetime="2014-07-30T14:52:25+02:00" is="relative-time">July 30, 2014</time>
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+          <a href="/sidiropoulos/galaxytools/commit/03ed1f1103f350fd4ab2b420252ae9245ffd7808" class="message" data-pjax="true" title="bigWig to Wig converter.">bigWig to Wig converter.</a>
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+             <span id="L1" rel="#L1">1</span>
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+
+           </td>
+           <td class="blob-line-code"><div class="code-body highlight"><pre><div class='line' id='LC1'><span class="nt">&lt;tool</span> <span class="na">id=</span><span class="s">&quot;bigwig_to_wig&quot;</span> <span class="na">name=</span><span class="s">&quot;BigWig to Wig&quot;</span> <span class="na">version=</span><span class="s">&quot;1.0.0&quot;</span><span class="nt">&gt;</span></div><div class='line' id='LC2'>&nbsp;&nbsp;<span class="nt">&lt;description&gt;</span>converter<span class="nt">&lt;/description&gt;</span></div><div class='line' id='LC3'>&nbsp;&nbsp;<span class="nt">&lt;command&gt;</span>/home/jens/bin/bigwig2wig_stdout -f $input -b $bin_size -l $mylab &gt; $output </div><div class='line' id='LC4'>&nbsp;&nbsp;<span class="nt">&lt;/command&gt;</span></div><div class='line' id='LC5'>&nbsp;&nbsp;<span class="nt">&lt;requirements&gt;</span></div><div class='line' id='LC6'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;requirement</span> <span class="na">type=</span><span class="s">&quot;package&quot;</span><span class="nt">&gt;</span>bigWigSummary<span class="nt">&lt;/requirement&gt;</span></div><div class='line' id='LC7'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;requirement</span> <span class="na">type=</span><span class="s">&quot;package&quot;</span><span class="nt">&gt;</span>bigwig2wig<span class="nt">&lt;/requirement&gt;</span></div><div class='line' id='LC8'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;requirement</span> <span class="na">type=</span><span class="s">&quot;package&quot;</span><span class="nt">&gt;</span>bigWigInfo<span class="nt">&lt;/requirement&gt;</span></div><div class='line' id='LC9'>&nbsp;&nbsp;<span class="nt">&lt;/requirements&gt;</span></div><div class='line' id='LC10'>&nbsp;&nbsp;<span class="nt">&lt;inputs&gt;</span></div><div class='line' id='LC11'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;param</span> <span class="na">format=</span><span class="s">&quot;bigwig&quot;</span> <span class="na">name=</span><span class="s">&quot;input&quot;</span> <span class="na">type=</span><span class="s">&quot;data&quot;</span> <span class="na">label=</span><span class="s">&quot;BigWig file to convert&quot;</span><span class="nt">&gt;</span></div><div class='line' id='LC12'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;/param&gt;</span></div><div class='line' id='LC13'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;param</span> <span class="na">name=</span><span class="s">&quot;bin_size&quot;</span> <span class="na">size=</span><span class="s">&quot;4&quot;</span> <span class="na">type=</span><span class="s">&quot;integer&quot;</span> <span class="na">value=</span><span class="s">&quot;500&quot;</span> <span class="na">label=</span><span class="s">&quot;Bin size&quot;</span> <span class="na">help=</span><span class="s">&quot;Must be an even integer &gt; 100.&quot;</span> <span class="nt">/&gt;</span></div><div class='line' id='LC14'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;param</span> <span class="na">name=</span><span class="s">&quot;mylab&quot;</span> <span class="na">type=</span><span class="s">&quot;text&quot;</span> <span class="na">value=</span><span class="s">&quot;wiggle_file&quot;</span> <span class="na">label=</span><span class="s">&quot;Output file prefix&quot;</span> <span class="na">help=</span><span class="s">&quot;&quot;</span> <span class="nt">/&gt;</span></div><div class='line' id='LC15'>&nbsp;&nbsp;<span class="nt">&lt;/inputs&gt;</span></div><div class='line' id='LC16'>&nbsp;&nbsp;<span class="nt">&lt;outputs&gt;</span></div><div class='line' id='LC17'>&nbsp;&nbsp;&nbsp;&nbsp;<span class="nt">&lt;data</span> <span class="na">format=</span><span class="s">&quot;wig&quot;</span> <span class="na">name=</span><span class="s">&quot;output&quot;</span> <span class="na">label=</span><span class="s">&quot;${mylab}_density_bin${bin_size}.wig&quot;</span> <span class="nt">/&gt;</span></div><div class='line' id='LC18'>&nbsp;&nbsp;<span class="nt">&lt;/outputs&gt;</span></div><div class='line' id='LC19'>&nbsp;&nbsp;<span class="nt">&lt;tests&gt;</span></div><div class='line' id='LC20'>&nbsp;&nbsp;<span class="nt">&lt;/tests&gt;</span></div><div class='line' id='LC21'>&nbsp;&nbsp;<span class="nt">&lt;help&gt;</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">&lt;/help&gt;</span></div><div class='line' id='LC32'><span class="nt">&lt;/tool&gt;</span></div></pre></div></td>
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