changeset 7:ee541c1852da

Uploaded version 2.1.0
author vipints
date Thu, 23 Apr 2015 17:43:11 -0400
parents 154887a3d92f
children d4f9b7beb52f
files GFFtools-GX
diffstat 1 files changed, 959 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GFFtools-GX	Thu Apr 23 17:43:11 2015 -0400
@@ -0,0 +1,959 @@
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+</form>
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+          <div class="site" itemscope itemtype="http://schema.org/WebPage">
+    <div id="js-flash-container">
+      
+    </div>
+    <div class="pagehead repohead instapaper_ignore readability-menu">
+      <div class="container">
+        
+<ul class="pagehead-actions">
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+    class="btn btn-sm btn-with-count tooltipped tooltipped-n"
+    aria-label="You must be signed in to watch a repository" rel="nofollow">
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+    Watch
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+    class="btn btn-sm btn-with-count tooltipped tooltipped-n"
+    aria-label="You must be signed in to star a repository" rel="nofollow">
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+        class="btn btn-sm btn-with-count tooltipped tooltipped-n"
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+    </li>
+</ul>
+
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+          <span class="mega-octicon octicon-repo"></span>
+          <span class="author"><a href="/vipints" class="url fn" itemprop="url" rel="author"><span itemprop="title">vipints</span></a></span><!--
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+
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+     role="navigation"
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+     data-issue-count-url="/vipints/GFFtools-GX/issues/counts">
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+    <li class="tooltipped tooltipped-w" aria-label="Code">
+      <a href="/vipints/GFFtools-GX" aria-label="Code" class="selected js-selected-navigation-item sunken-menu-item" data-hotkey="g c" data-selected-links="repo_source repo_downloads repo_commits repo_releases repo_tags repo_branches /vipints/GFFtools-GX">
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+    <li class="tooltipped tooltipped-w" aria-label="Pull requests">
+      <a href="/vipints/GFFtools-GX/pulls" aria-label="Pull requests" class="js-selected-navigation-item sunken-menu-item" data-hotkey="g p" data-selected-links="repo_pulls /vipints/GFFtools-GX/pulls">
+          <span class="octicon octicon-git-pull-request"></span> <span class="full-word">Pull requests</span>
+          <span class="js-pull-replace-counter"></span>
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+    <li class="tooltipped tooltipped-w" aria-label="Graphs">
+      <a href="/vipints/GFFtools-GX/graphs" aria-label="Graphs" class="js-selected-navigation-item sunken-menu-item" data-selected-links="repo_graphs repo_contributors /vipints/GFFtools-GX/graphs">
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+</a>    </li>
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+
+
+</nav>
+
+              <div class="only-with-full-nav">
+                  
+<div class="clone-url open"
+  data-protocol-type="http"
+  data-url="/users/set_protocol?protocol_selector=http&amp;protocol_type=clone">
+  <h3><span class="text-emphasized">HTTPS</span> clone URL</h3>
+  <div class="input-group js-zeroclipboard-container">
+    <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
+           value="https://github.com/vipints/GFFtools-GX.git" readonly="readonly">
+    <span class="input-group-button">
+      <button aria-label="Copy to clipboard" class="js-zeroclipboard btn btn-sm zeroclipboard-button tooltipped tooltipped-s" data-copied-hint="Copied!" type="button"><span class="octicon octicon-clippy"></span></button>
+    </span>
+  </div>
+</div>
+
+  
+<div class="clone-url "
+  data-protocol-type="subversion"
+  data-url="/users/set_protocol?protocol_selector=subversion&amp;protocol_type=clone">
+  <h3><span class="text-emphasized">Subversion</span> checkout URL</h3>
+  <div class="input-group js-zeroclipboard-container">
+    <input type="text" class="input-mini input-monospace js-url-field js-zeroclipboard-target"
+           value="https://github.com/vipints/GFFtools-GX" readonly="readonly">
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+    </span>
+  </div>
+</div>
+
+
+
+<p class="clone-options">You can clone with
+  <a href="#" class="js-clone-selector" data-protocol="http">HTTPS</a> or <a href="#" class="js-clone-selector" data-protocol="subversion">Subversion</a>.
+  <a href="https://help.github.com/articles/which-remote-url-should-i-use" class="help tooltipped tooltipped-n" aria-label="Get help on which URL is right for you.">
+    <span class="octicon octicon-question"></span>
+  </a>
+</p>
+
+
+
+
+                <a href="/vipints/GFFtools-GX/archive/master.zip"
+                   class="btn btn-sm sidebar-button"
+                   aria-label="Download the contents of vipints/GFFtools-GX as a zip file"
+                   title="Download the contents of vipints/GFFtools-GX as a zip file"
+                   rel="nofollow">
+                  <span class="octicon octicon-cloud-download"></span>
+                  Download ZIP
+                </a>
+              </div>
+        </div><!-- /.repository-sidebar -->
+
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+          
+<span id="js-show-full-navigation"></span>
+
+<div class="repository-meta js-details-container ">
+    <div class="repository-description">
+      gfftools - Galaxy toolshed repository
+    </div>
+
+
+
+</div>
+
+<div class="overall-summary overall-summary-bottomless">
+
+  <div class="stats-switcher-viewport js-stats-switcher-viewport">
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+    <ul class="numbers-summary">
+      <li class="commits">
+        <a data-pjax href="/vipints/GFFtools-GX/commits/master">
+            <span class="octicon octicon-history"></span>
+            <span class="num text-emphasized">
+              103
+            </span>
+            commits
+        </a>
+      </li>
+      <li>
+        <a data-pjax href="/vipints/GFFtools-GX/branches">
+          <span class="octicon octicon-git-branch"></span>
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+            1
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+          branch
+        </a>
+      </li>
+
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+        <a data-pjax href="/vipints/GFFtools-GX/releases">
+          <span class="octicon octicon-tag"></span>
+          <span class="num text-emphasized">
+            0
+          </span>
+          releases
+        </a>
+      </li>
+
+      <li>
+        
+  <a href="/vipints/GFFtools-GX/graphs/contributors">
+    <span class="octicon octicon-organization"></span>
+    <span class="num text-emphasized">
+      1
+    </span>
+    contributor
+  </a>
+      </li>
+    </ul>
+
+      <div class="repository-lang-stats">
+        <ol class="repository-lang-stats-numbers">
+          <li>
+              <a href="/vipints/GFFtools-GX/search?l=python">
+                <span class="color-block language-color" style="background-color:#3581ba;"></span>
+                <span class="lang">Python</span>
+                <span class="percent">100%</span>
+              </a>
+          </li>
+        </ol>
+      </div>
+    </div>
+  </div>
+
+</div>
+
+  <div class="repository-lang-stats-graph js-toggle-lang-stats" title="Click for language details">
+    <span class="language-color" aria-label="Python 100%" style="width:100%; background-color:#3581ba;" itemprop="keywords">Python</span>
+  </div>
+
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+
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+  <a href="/vipints/GFFtools-GX/find/master"
+        class="js-show-file-finder btn btn-sm empty-icon tooltipped tooltipped-s right"
+        data-pjax
+        data-hotkey="t"
+        aria-label="Quickly jump between files">
+    <span class="octicon octicon-list-unordered"></span>
+  </a>
+    <a href="/vipints/GFFtools-GX/compare" aria-label="Compare, review, create a pull request" class="btn btn-sm btn-primary tooltipped tooltipped-se left compare-button" aria-label="Compare &amp; review" data-pjax data-ga-click="Repository, go to compare view, location:repo overview; icon:git-compare">
+      <span class="octicon octicon-git-compare"></span>
+    </a>
+
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+<div class="select-menu js-menu-container js-select-menu left">
+  <span class="btn btn-sm select-menu-button js-menu-target css-truncate" data-hotkey="w"
+    data-master-branch="master"
+    data-ref="master"
+    title="master"
+    role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true">
+    <span class="octicon octicon-git-branch"></span>
+    <i>branch:</i>
+    <span class="js-select-button css-truncate-target">master</span>
+  </span>
+
+  <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true">
+
+    <div class="select-menu-modal">
+      <div class="select-menu-header">
+        <span class="select-menu-title">Switch branches/tags</span>
+        <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span>
+      </div>
+
+      <div class="select-menu-filters">
+        <div class="select-menu-text-filter">
+          <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags">
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+        <div class="select-menu-tabs">
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+              <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab">Branches</a>
+            </li>
+            <li class="select-menu-tab">
+              <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab">Tags</a>
+            </li>
+          </ul>
+        </div>
+      </div>
+
+      <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches">
+
+        <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring">
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+            <a class="select-menu-item js-navigation-item js-navigation-open selected"
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+               data-name="master"
+               data-skip-pjax="true"
+               rel="nofollow">
+              <span class="select-menu-item-icon octicon octicon-check"></span>
+              <span class="select-menu-item-text css-truncate-target" title="master">
+                master
+              </span>
+            </a>
+        </div>
+
+          <div class="select-menu-no-results">Nothing to show</div>
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+      <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="sha-block" data-pjax>latest commit <span class="sha">0ea921f8d7</span></a>
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+        <span class="author-name"><a href="/vipints" rel="author">vipints</a></span>
+        authored <time class="updated" datetime="2015-04-23T21:27:17Z" is="relative-time">Apr 23, 2015</time>
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+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/tree/master/test-data" class="js-directory-link" id="24346e1b50066607059af36e3b684b24-99e7a2029aade02cb90a0e26ff6109547a6078ea" title="test-data">test-data</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/46e670f9d93f3797740d21a100428fe195b6c83f" class="message" data-pjax="true" title="functional test perfomed after the change">functional test perfomed after the change</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:42:01Z" is="time-ago">Apr 21, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/.gitignore" class="js-directory-link" id="a084b794bc0759e7a6b77810e01874f2-0334fc9da4d9b7a262012ae6cae37002259af5b2" title=".gitignore">.gitignore</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/c5b661defaf94700cf290651669846c8258e220d" class="message" data-pjax="true" title="ignored pyc and swap files">ignored pyc and swap files</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2014-07-18T22:28:50Z" is="time-ago">Jul 18, 2014</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/GFFParser.py" class="js-directory-link" id="4a9c2f3a2b51d00c039e9951aa5df3fd-505eece57e21af803c93cdb06d9d569c81d1d811" title="GFFParser.py">GFFParser.py</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF f…</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/README.md" class="js-directory-link" id="04c6e90faac2675aa89e2176d2eec7d8-17e766c0f2926d94933cb7320afd6c1f5db293fb" title="README.md">README.md</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="message" data-pjax="true" title="fixed">fixed</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-23T21:27:17Z" is="time-ago">Apr 23, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.py" class="js-directory-link" id="4fd14b034003e6ed6b3c1243f3f285ed-461ae7292d229b40fb98dec1d28a67aebfde7c96" title="bed_to_gff.py">bed_to_gff.py</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/b882fc8c206c3203792da6c4c856005eb06934c4" class="message" data-pjax="true" title="removing print statement from the code">removing print statement from the code</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-14T23:41:11Z" is="time-ago">Apr 14, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.xml" class="js-directory-link" id="fd45df94f6d642a741c0c8d038949b37-2b5908455dd6730bd4bbd634f56316dfd70eca03" title="bed_to_gff.xml">bed_to_gff.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.py" class="js-directory-link" id="8cedf4409efd74682d25ee79bb3574dc-6638d994bf8d1a8aaa231c70bf44b6021f9ccf1b" title="gbk_to_gff.py">gbk_to_gff.py</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/84a145c7ee9efa171dbe1d64223e20ceb1930de6" class="message" data-pjax="true" title="gbk parsing and correctly assigning feature type">gbk parsing and correctly assigning feature type</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:04:25Z" is="time-ago">Apr 17, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.xml" class="js-directory-link" id="5e708155a06e4244e26c978ed02c6fd2-c90e390761eb5390bda2e245b7eb7456d5e9c665" title="gbk_to_gff.xml">gbk_to_gff.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.py" class="js-directory-link" id="95b17a03c0948b20d1264fcd269b60fa-457e6d44dbc1f4531de174641f74f9e6ec689982" title="gff_to_bed.py">gff_to_bed.py</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/f84e0d96db79436b685066c088bf1555a3bf29e1" class="message" data-pjax="true" title="changing the float behaviour to int">changing the float behaviour to int</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-22T16:25:13Z" is="time-ago">Apr 22, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.xml" class="js-directory-link" id="8c7d5ae4b79728262acfc56888f2444e-10754bece6a7a5a7c5dc9d533d92ddfa046e6b6b" title="gff_to_bed.xml">gff_to_bed.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/2c96e399526d372a61df5b4068bc91e08af49092" class="message" data-pjax="true" title="updated the wrapper version">updated the wrapper version</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T02:59:32Z" is="time-ago">Apr 18, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.py" class="js-directory-link" id="88b7a441373dfec1e07cd28bb1eb8c3e-9ff53c56125edfa286255f489e61cda154a21693" title="gff_to_gtf.py">gff_to_gtf.py</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.xml" class="js-directory-link" id="f4676750a1f71b9fbf35b537b0546842-a2b41ec7924d6609f219bdf8c0372af59ea747d2" title="gff_to_gtf.xml">gff_to_gtf.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.py" class="js-directory-link" id="6989ac39182645599caeb47b4e0e8ef6-6d786691f74f0c00db3da883f4e6e7e1d009d2c2" title="gtf_to_gff.py">gtf_to_gff.py</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.xml" class="js-directory-link" id="a8bd25db400514c2556192045eacd820-dc2031de1c3daa1cf8644a5c62c9d4afce97ad39" title="gtf_to_gff.xml">gtf_to_gff.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/helper.py" class="js-directory-link" id="702b6abf015bfdb4e41308ddd3b297a9-a711ed60defe1bd9ef579fada75e32da2313935c" title="helper.py">helper.py</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF f…</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_conf.xml.sample" class="js-directory-link" id="76a06ab03a6f35bfb6ff2be40e654b7e-e26478f762dbc5e03f339bc5598086009e4f8be0" title="tool_conf.xml.sample">tool_conf.xml.sample</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/04ccdc96c4bf8d6b8420a05c9afa8c8540345e32" class="message" data-pjax="true" title="updated the toolpanel list">updated the toolpanel list</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:15:28Z" is="time-ago">Apr 20, 2015</time></span>
+          </td>
+        </tr>
+        <tr>
+          <td class="icon">
+            <span class="octicon octicon-file-text"></span>
+            <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" />
+          </td>
+          <td class="content">
+            <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_dependencies.xml" class="js-directory-link" id="1f1e2fcbf1ddc07a88bc59ca246c9a90-a0a1a7f1bb7e1a6a8b79f30629c8968f8b4c8d36" title="tool_dependencies.xml">tool_dependencies.xml</a></span>
+          </td>
+          <td class="message">
+            <span class="css-truncate css-truncate-target">
+              <a href="/vipints/GFFtools-GX/commit/c75c2be2f54ca59449e999346de2427584789ec9" class="message" data-pjax="true" title="biopython required">biopython required</a>
+            </span>
+          </td>
+          <td class="age">
+            <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:54:33Z" is="time-ago">Apr 21, 2015</time></span>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+</div>
+
+
+  <div id="readme" class="boxed-group flush clearfix announce instapaper_body md">
+    <h3>
+      <span class="octicon octicon-book"></span>
+      README.md
+    </h3>
+
+    <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1>
+<a id="user-content-gfftools-gx-" class="anchor" href="#gfftools-gx-" aria-hidden="true"><span class="octicon octicon-link"></span></a>GFFtools-GX </h1>
+
+<p>A collection of tools for converting genome annotation between <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format4">GTF</a>, <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a>, <a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html">GenBank</a> and <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format3">GFF</a>.</p>
+
+<h5>
+<a id="user-content-introduction" class="anchor" href="#introduction" aria-hidden="true"><span class="octicon octicon-link"></span></a>INTRODUCTION</h5>
+
+<p>Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like <a href="http://www.ensembl.org">ENSEMBL</a>, <a href="https://genome.ucsc.edu/">UCSC</a>, <a href="http://genome.jgi.doe.gov/">JGI</a> and <a href="http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/HelpJan.html">NCBI AceView</a>. These programs can be easily integrated into your galaxy instance.</p>
+
+<h5>
+<a id="user-content-contents" class="anchor" href="#contents" aria-hidden="true"><span class="octicon octicon-link"></span></a>CONTENTS</h5>
+
+<p>Included utilities are: </p>
+
+<pre><code>BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
+GBK-to-GFF: convert data from genbank format to GFF
+GFF-to-BED: convert data from GFF to 12 column BED format
+GFF-to-GTF: convert data from GFF to GTF 
+GTF-to-GFF: convert data from GTF to valid GFF
+</code></pre>
+
+<p>test-data: Test data set. (move to your galaxy-root-folder/test-data/)</p>
+
+<pre><code>You may need to move the test files into your test-data directory so galaxy can find them. 
+If you want to run the functional tests eg as: 
+
+exmaple: 
+sh run_functional_tests.sh -id fml_gtf2gff
+</code></pre>
+
+<h5>
+<a id="user-content-requirements" class="anchor" href="#requirements" aria-hidden="true"><span class="octicon octicon-link"></span></a>REQUIREMENTS</h5>
+
+<pre><code>python2.6 or 2.7 and biopython  
+
+Galaxy should be able to automatically install biopython via Galaxy toolshed.
+</code></pre>
+
+<h5>
+<a id="user-content-commentsquestions" class="anchor" href="#commentsquestions" aria-hidden="true"><span class="octicon octicon-link"></span></a>COMMENTS/QUESTIONS</h5>
+
+<p>I can be reached at vipin [at] cbio.mskcc.org </p>
+
+<h5>
+<a id="user-content-license" class="anchor" href="#license" aria-hidden="true"><span class="octicon octicon-link"></span></a>LICENSE</h5>
+
+<p>Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society</p>
+
+<pre><code>          2013-2015, Memorial Sloan Kettering Cancer Center
+          Vipin T Sreedharan &lt;vipin@cbio.mskcc.org&gt;  
+</code></pre>
+
+<p>All rights reserved.</p>
+
+<p>Licensed under the BSD 2-Clause License: <a href="http://opensource.org/licenses/BSD-2-Clause">http://opensource.org/licenses/BSD-2-Clause</a></p>
+
+<pre><code>Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+    * Redistributions of source code must retain the above copyright notice,
+      this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above copyright notice,
+      this list of conditions and the following disclaimer in the documentation
+      and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+</code></pre>
+
+<h5>
+<a id="user-content-courtesy" class="anchor" href="#courtesy" aria-hidden="true"><span class="octicon octicon-link"></span></a>COURTESY</h5>
+
+<p>To the Galaxy Team.</p>
+</article>
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