Mercurial > repos > devteam > samtools_sort
changeset 1:a7b6e385a895
Deleted selected files
| author | devteam |
|---|---|
| date | Wed, 10 Sep 2014 23:08:46 -0400 |
| parents | 4cafbe1d2ea6 |
| children | 5c01430e6e76 |
| files | samtools_sort.xml tool_dependencies.xml |
| diffstat | 2 files changed, 0 insertions(+), 1626 deletions(-) [+] |
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--- a/samtools_sort.xml Wed Sep 10 23:06:15 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,899 +0,0 @@ - - - - -<!DOCTYPE html> -<html lang="en" 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"> - <meta http-equiv="Content-Language" content="en"> - - - <title>galaxytools/samtools_sort.xml at master · bgruening/galaxytools</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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</tr> - <tr> - <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> - <td id="LC2" class="blob-code js-file-line"> <span class="nt"><requirements></span></td> - </tr> - <tr> - <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> - <td id="LC3" class="blob-code js-file-line"> <span class="nt"><requirement</span> <span class="na">type=</span><span class="s">"package"</span> <span class="na">version=</span><span class="s">"0.1.19"</span><span class="nt">></span>samtools<span class="nt"></requirement></span></td> - </tr> - <tr> - <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> - <td id="LC4" class="blob-code js-file-line"> <span class="nt"></requirements></span></td> - </tr> - <tr> - <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> - <td id="LC5" class="blob-code js-file-line"> <span class="nt"><description></span>a BAM file<span class="nt"></description></span></td> - </tr> - <tr> - <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> - <td id="LC6" class="blob-code js-file-line"> <span class="nt"><command></span></td> - </tr> - <tr> - <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> - <td id="LC7" class="blob-code js-file-line"> samtools sort</td> - </tr> - <tr> - <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> - <td id="LC8" class="blob-code js-file-line"> $sort_mode</td> - </tr> - <tr> - <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> - <td id="LC9" class="blob-code js-file-line"> "${input1}" foo</td> - </tr> - <tr> - <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> - <td id="LC10" class="blob-code js-file-line"> 2<span class="ni">&gt;&amp;</span>1 || echo "Error running samtools sort." <span class="ni">&gt;&amp;</span>2</td> - </tr> - <tr> - <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> - <td id="LC11" class="blob-code js-file-line"> ;</td> - </tr> - <tr> - <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> - <td id="LC12" class="blob-code js-file-line"> mv foo.bam "${output1}"</td> - </tr> - <tr> - <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> - <td id="LC13" class="blob-code js-file-line"> <span class="nt"></command></span></td> - </tr> - <tr> - <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> - <td id="LC14" class="blob-code js-file-line"> <span class="nt"><inputs></span></td> - </tr> - <tr> - <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> - <td id="LC15" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"input1"</span> <span class="na">type=</span><span class="s">"data"</span> <span class="na">format=</span><span class="s">"bam"</span> <span class="na">label=</span><span class="s">"BAM File"</span> <span class="nt">/></span></td> - </tr> - <tr> - <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> - <td id="LC16" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"sort_mode"</span> <span class="na">type=</span><span class="s">"select"</span> <span class="na">label=</span><span class="s">"Sort by "</span><span class="nt">></span></td> - </tr> - <tr> - <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> - <td id="LC17" class="blob-code js-file-line"> <span class="nt"><option</span> <span class="na">value=</span><span class="s">""</span> <span class="na">selected=</span><span class="s">"True"</span><span class="nt">></span>Chromosomal coordinates<span class="nt"></option></span></td> - </tr> - <tr> - <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> - <td id="LC18" class="blob-code js-file-line"> <span class="nt"><option</span> <span class="na">value=</span><span class="s">"-n"</span><span class="nt">></span>Read names<span class="nt"></option></span></td> - </tr> - <tr> - <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> - <td id="LC19" class="blob-code js-file-line"> <span class="nt"></param></span></td> - </tr> - <tr> - <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> - <td id="LC20" class="blob-code js-file-line"> <span class="nt"></inputs></span></td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code js-file-line"> <span class="nt"><outputs></span></td> - </tr> - <tr> - <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> - <td id="LC22" class="blob-code js-file-line"> <span class="nt"><data</span> <span class="na">name=</span><span class="s">"output1"</span> <span class="na">format=</span><span class="s">"bam"</span> <span class="nt">/></span></td> - </tr> - <tr> - <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> - <td id="LC23" class="blob-code js-file-line"> <span class="nt"></outputs></span></td> - </tr> - <tr> - <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> - <td id="LC24" class="blob-code js-file-line"> <span class="nt"><tests></span></td> - </tr> - <tr> - <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> - <td id="LC25" class="blob-code js-file-line"> <span class="nt"><test></span></td> - </tr> - <tr> - <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> - <td id="LC26" class="blob-code js-file-line"> <span class="nt"><param</span> <span class="na">name=</span><span class="s">"input1"</span> <span class="na">value=</span><span class="s">"1.bam"</span> <span class="na">ftype=</span><span class="s">"bam"</span> <span class="nt">/></span></td> - </tr> - <tr> - <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> - <td id="LC27" class="blob-code js-file-line"> <span class="nt"><output</span> <span class="na">name=</span><span class="s">"output1"</span> <span class="na">file=</span><span class="s">"1_sort.bam"</span> <span class="na">ftype=</span><span class="s">"bam"</span> <span class="na">sort=</span><span class="s">"True"</span><span class="nt">/></span></td> - </tr> - <tr> - <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> - <td id="LC28" class="blob-code js-file-line"> <span class="nt"></test></span></td> - </tr> - <tr> - <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> - <td id="LC29" class="blob-code js-file-line"> <span class="nt"></tests></span></td> - </tr> - <tr> - <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> - <td id="LC30" class="blob-code js-file-line"> <span class="nt"><help></span></td> - </tr> - <tr> - <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> - <td id="LC31" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> - <td id="LC32" class="blob-code js-file-line">**What it does**</td> - </tr> - <tr> - <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> - <td id="LC33" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> - <td id="LC34" class="blob-code js-file-line">This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.</td> - </tr> - <tr> - <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> - <td id="LC35" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> - <td id="LC36" class="blob-code js-file-line">.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml</td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code js-file-line">------</td> - </tr> - <tr> - <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> - <td id="LC39" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> - <td id="LC40" class="blob-code js-file-line">**Citation**</td> - </tr> - <tr> - <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> - <td id="LC41" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> - <td id="LC42" class="blob-code js-file-line">For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <span class="ni">&lt;</span>http://www.ncbi.nlm.nih.gov/pubmed/19505943<span class="ni">&gt;</span>`_</td> - </tr> - <tr> - <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> - <td id="LC43" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code js-file-line">If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*</td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code js-file-line"> <span class="nt"></help></span></td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code js-file-line"><span class="nt"></tool></span></td> - </tr> -</table> - - </div> - - </div> -</div> - -<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> -<div id="jump-to-line" style="display:none"> - <form accept-charset="UTF-8" class="js-jump-to-line-form"> - <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> - <button type="submit" class="button">Go</button> - </form> -</div> - - </div> - - </div><!-- /.repo-container --> - <div class="modal-backdrop"></div> - </div><!-- /.container --> - </div><!-- /.site --> - - - </div><!-- /.wrapper --> - - <div class="container"> - <div class="site-footer"> - <ul class="site-footer-links right"> - <li><a href="https://status.github.com/">Status</a></li> - <li><a href="http://developer.github.com">API</a></li> - <li><a href="http://training.github.com">Training</a></li> - <li><a href="http://shop.github.com">Shop</a></li> - <li><a href="/blog">Blog</a></li> - <li><a href="/about">About</a></li> - - </ul> - - <a href="/" aria-label="Homepage"> - <span class="mega-octicon octicon-mark-github" title="GitHub"></span> - </a> - - <ul class="site-footer-links"> - <li>© 2014 <span title="0.04104s from github-fe135-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> - <li><a href="/site/terms">Terms</a></li> - <li><a href="/site/privacy">Privacy</a></li> - <li><a href="/security">Security</a></li> - <li><a href="/contact">Contact</a></li> - </ul> - </div><!-- /.site-footer --> -</div><!-- /.container --> - - - <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> - <div class="fullscreen-container js-suggester-container"> - <div class="textarea-wrap"> - <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents js-suggester-field" placeholder=""></textarea> - </div> - </div> - <div class="fullscreen-sidebar"> - <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> - <span class="mega-octicon octicon-screen-normal"></span> - </a> - <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" - aria-label="Switch themes"> - <span class="octicon octicon-color-mode"></span> - </a> - </div> -</div> - - - - <div id="ajax-error-message" class="flash flash-error"> - <span class="octicon octicon-alert"></span> - <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> - Something went wrong with that request. 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</div> -</div> - - - <div class="commit file-history-tease"> - <div class="file-history-tease-header"> - <img alt="Björn Grüning" class="avatar" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" /> - <span class="author"><a href="/bgruening" rel="author">bgruening</a></span> - <time datetime="2014-06-20T17:05:21+02:00" is="relative-time">June 20, 2014</time> - <div class="commit-title"> - <a href="/bgruening/galaxytools/commit/7e2a1f1f8338602cba2ae409df31b92bd12a97d6" class="message" data-pjax="true" title="add samtools sort">add samtools sort</a> - </div> - </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="Björn Grüning" data-user="469983" height="24" src="https://avatars1.githubusercontent.com/u/469983?v=2&s=48" width="24" /> - 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