Mercurial > repos > yating-l > hubarchivecreator
diff doc/_build/html/code.html @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
|---|---|
| date | Wed, 21 Dec 2016 12:13:04 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/doc/_build/html/code.html Wed Dec 21 12:13:04 2016 -0500 @@ -0,0 +1,227 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + + +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + + <title>Auto Generated Documentation — HubArchiveCreator 2.3 documentation</title> + + <link rel="stylesheet" href="_static/classic.css" type="text/css" /> + <link rel="stylesheet" href="_static/pygments.css" type="text/css" /> + + <script type="text/javascript"> + var DOCUMENTATION_OPTIONS = { + URL_ROOT: './', + VERSION: '2.3', + COLLAPSE_INDEX: false, + FILE_SUFFIX: '.html', + HAS_SOURCE: true + }; + </script> + <script type="text/javascript" src="_static/jquery.js"></script> + <script type="text/javascript" src="_static/underscore.js"></script> + <script type="text/javascript" src="_static/doctools.js"></script> + <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> + <link rel="index" title="Index" href="genindex.html" /> + <link rel="search" title="Search" href="search.html" /> + <link rel="top" title="HubArchiveCreator 2.3 documentation" href="index.html" /> + <link rel="prev" title="Welcome to HubArchiveCreator’s documentation!" href="index.html" /> + </head> + <body role="document"> + <div class="related" role="navigation" aria-label="related navigation"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + accesskey="I">index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="index.html" title="Welcome to HubArchiveCreator’s documentation!" + accesskey="P">previous</a> |</li> + <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li> + </ul> + </div> + + <div class="document"> + <div class="documentwrapper"> + <div class="bodywrapper"> + <div class="body" role="main"> + + <div class="section" id="module-hubArchiveCreator"> +<span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-hubArchiveCreator" title="Permalink to this headline">¶</a></h1> +<p>This Galaxy tool permits to prepare your files to be ready for +Assembly Hub visualization. +Program test arguments: +hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</p> +<dl class="function"> +<dt id="hubArchiveCreator.configure_logger_dev"> +<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_dev</code><span class="sig-paren">(</span><em>log_stdout=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#configure_logger_dev"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.configure_logger_dev" title="Permalink to this definition">¶</a></dt> +<dd><dl class="docutils"> +<dt>Dev Logger is defined as following:</dt> +<dd><ul class="first last simple"> +<li>Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout</li> +<li>Still access to full, brute and traceback in stderr for errors</li> +<li>And further access to debug if needed</li> +</ul> +</dd> +</dl> +</dd></dl> + +<dl class="function"> +<dt id="hubArchiveCreator.configure_logger_stderr"> +<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_stderr</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#configure_logger_stderr"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.configure_logger_stderr" title="Permalink to this definition">¶</a></dt> +<dd><p>Configure what should be logged in stderr</p> +</dd></dl> + +<dl class="function"> +<dt id="hubArchiveCreator.configure_logger_user"> +<code class="descclassname">hubArchiveCreator.</code><code class="descname">configure_logger_user</code><span class="sig-paren">(</span><em>log_stdout=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#configure_logger_user"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.configure_logger_user" title="Permalink to this definition">¶</a></dt> +<dd><dl class="docutils"> +<dt>User Logger is defined as following:</dt> +<dd><ul class="first last"> +<li><dl class="first docutils"> +<dt>User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback</dt> +<dd><p class="first last">in STDOUT</p> +</dd> +</dl> +</li> +<li><dl class="first docutils"> +<dt>Still access to full, brute and traceback for errors</dt> +<dd><p class="first last">in STDERR</p> +</dd> +</dl> +</li> +<li><dl class="first docutils"> +<dt>And further access to debug if needed</dt> +<dd><p class="first last">in .log</p> +</dd> +</dl> +</li> +</ul> +</dd> +</dl> +</dd></dl> + +<dl class="function"> +<dt id="hubArchiveCreator.create_ordered_datatype_objects"> +<code class="descclassname">hubArchiveCreator.</code><code class="descname">create_ordered_datatype_objects</code><span class="sig-paren">(</span><em>ExtensionClass</em>, <em>array_inputs</em>, <em>inputs_data</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#create_ordered_datatype_objects"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.create_ordered_datatype_objects" title="Permalink to this definition">¶</a></dt> +<dd><p>Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub +and update the dictionary of datatype</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple"> +<li><strong>ExtensionClass</strong> (<em>Datatype</em>) – </li> +<li><strong>array_inputs</strong> (<em>list[string]</em>) – </li> +<li><strong>inputs_data</strong> (<a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#dict" title="(in Python v2.7)"><em>dict</em></a>) – </li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#dict" title="(in Python v2.7)">dict</a></p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + +<dl class="function"> +<dt id="hubArchiveCreator.sanitize_name_input"> +<code class="descclassname">hubArchiveCreator.</code><code class="descname">sanitize_name_input</code><span class="sig-paren">(</span><em>string_to_sanitize</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#sanitize_name_input"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.sanitize_name_input" title="Permalink to this definition">¶</a></dt> +<dd><p>Sanitize the string passed in parameter by replacing ‘/’ and ‘ ‘ by ‘_’</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>string_to_sanitize</strong> – </td> +</tr> +</tbody> +</table> +<p>:return :</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Example:</th><td class="field-body"></td> +</tr> +</tbody> +</table> +<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">sanitize_name_input</span><span class="p">(</span><span class="s1">'this/is an//example'</span><span class="p">)</span> +<span class="go">this_is_an__example</span> +</pre></div> +</div> +</dd></dl> + +<dl class="function"> +<dt id="hubArchiveCreator.sanitize_name_inputs"> +<code class="descclassname">hubArchiveCreator.</code><code class="descname">sanitize_name_inputs</code><span class="sig-paren">(</span><em>inputs_data</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/hubArchiveCreator.html#sanitize_name_inputs"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#hubArchiveCreator.sanitize_name_inputs" title="Permalink to this definition">¶</a></dt> +<dd><p>Sanitize value of the keys “name” of the dictionary passed in parameter.</p> +<p>Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces. +Also, it can contain ‘/’ character and could break the use of os.path function.</p> +<table class="docutils field-list" frame="void" rules="none"> +<col class="field-name" /> +<col class="field-body" /> +<tbody valign="top"> +<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>inputs_data</strong> – dict[string, dict[string, string]]</td> +</tr> +</tbody> +</table> +</dd></dl> + +</div> + + + </div> + </div> + </div> + <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> + <div class="sphinxsidebarwrapper"> + <h4>Previous topic</h4> + <p class="topless"><a href="index.html" + title="previous chapter">Welcome to HubArchiveCreator’s documentation!</a></p> + <div role="note" aria-label="source link"> + <h3>This Page</h3> + <ul class="this-page-menu"> + <li><a href="_sources/code.txt" + rel="nofollow">Show Source</a></li> + </ul> + </div> +<div id="searchbox" style="display: none" role="search"> + <h3>Quick search</h3> + <form class="search" action="search.html" method="get"> + <div><input type="text" name="q" /></div> + <div><input type="submit" value="Go" /></div> + <input type="hidden" name="check_keywords" value="yes" /> + <input type="hidden" name="area" value="default" /> + </form> +</div> +<script type="text/javascript">$('#searchbox').show(0);</script> + </div> + </div> + <div class="clearer"></div> + </div> + <div class="related" role="navigation" aria-label="related navigation"> + <h3>Navigation</h3> + <ul> + <li class="right" style="margin-right: 10px"> + <a href="genindex.html" title="General Index" + >index</a></li> + <li class="right" > + <a href="py-modindex.html" title="Python Module Index" + >modules</a> |</li> + <li class="right" > + <a href="index.html" title="Welcome to HubArchiveCreator’s documentation!" + >previous</a> |</li> + <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> »</li> + </ul> + </div> + <div class="footer" role="contentinfo"> + © Copyright 2016, Remi Marenco. + Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8. + </div> + </body> +</html> \ No newline at end of file