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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
author yating-l
date Fri, 20 Jan 2017 17:12:03 -0500
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54 <div class="section" id="module-hubArchiveCreator">
55 <span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-hubArchiveCreator" title="Permalink to this headline">¶</a></h1>
56 <p>This Galaxy tool permits to prepare your files to be ready for
57 Assembly Hub visualization.
58 Program test arguments:
59 hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</p>
60 <dl class="function">
61 <dt id="hubArchiveCreator.configure_logger_dev">
62 <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>
63 <dd><dl class="docutils">
64 <dt>Dev Logger is defined as following:</dt>
65 <dd><ul class="first last simple">
66 <li>Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout</li>
67 <li>Still access to full, brute and traceback in stderr for errors</li>
68 <li>And further access to debug if needed</li>
69 </ul>
70 </dd>
71 </dl>
72 </dd></dl>
73
74 <dl class="function">
75 <dt id="hubArchiveCreator.configure_logger_stderr">
76 <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>
77 <dd><p>Configure what should be logged in stderr</p>
78 </dd></dl>
79
80 <dl class="function">
81 <dt id="hubArchiveCreator.configure_logger_user">
82 <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>
83 <dd><dl class="docutils">
84 <dt>User Logger is defined as following:</dt>
85 <dd><ul class="first last">
86 <li><dl class="first docutils">
87 <dt>User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback</dt>
88 <dd><p class="first last">in STDOUT</p>
89 </dd>
90 </dl>
91 </li>
92 <li><dl class="first docutils">
93 <dt>Still access to full, brute and traceback for errors</dt>
94 <dd><p class="first last">in STDERR</p>
95 </dd>
96 </dl>
97 </li>
98 <li><dl class="first docutils">
99 <dt>And further access to debug if needed</dt>
100 <dd><p class="first last">in .log</p>
101 </dd>
102 </dl>
103 </li>
104 </ul>
105 </dd>
106 </dl>
107 </dd></dl>
108
109 <dl class="function">
110 <dt id="hubArchiveCreator.create_ordered_datatype_objects">
111 <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>
112 <dd><p>Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
113 and update the dictionary of datatype</p>
114 <table class="docutils field-list" frame="void" rules="none">
115 <col class="field-name" />
116 <col class="field-body" />
117 <tbody valign="top">
118 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
119 <li><strong>ExtensionClass</strong> (<em>Datatype</em>) &#8211; </li>
120 <li><strong>array_inputs</strong> (<em>list[string]</em>) &#8211; </li>
121 <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>) &#8211; </li>
122 </ul>
123 </td>
124 </tr>
125 <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>
126 </td>
127 </tr>
128 </tbody>
129 </table>
130 </dd></dl>
131
132 <dl class="function">
133 <dt id="hubArchiveCreator.sanitize_name_input">
134 <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>
135 <dd><p>Sanitize the string passed in parameter by replacing &#8216;/&#8217; and &#8216; &#8216; by &#8216;_&#8217;</p>
136 <table class="docutils field-list" frame="void" rules="none">
137 <col class="field-name" />
138 <col class="field-body" />
139 <tbody valign="top">
140 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>string_to_sanitize</strong> &#8211; </td>
141 </tr>
142 </tbody>
143 </table>
144 <p>:return :</p>
145 <table class="docutils field-list" frame="void" rules="none">
146 <col class="field-name" />
147 <col class="field-body" />
148 <tbody valign="top">
149 <tr class="field-odd field"><th class="field-name">Example:</th><td class="field-body"></td>
150 </tr>
151 </tbody>
152 </table>
153 <div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">sanitize_name_input</span><span class="p">(</span><span class="s1">&#39;this/is an//example&#39;</span><span class="p">)</span>
154 <span class="go">this_is_an__example</span>
155 </pre></div>
156 </div>
157 </dd></dl>
158
159 <dl class="function">
160 <dt id="hubArchiveCreator.sanitize_name_inputs">
161 <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>
162 <dd><p>Sanitize value of the keys &#8220;name&#8221; of the dictionary passed in parameter.</p>
163 <p>Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
164 Also, it can contain &#8216;/&#8217; character and could break the use of os.path function.</p>
165 <table class="docutils field-list" frame="void" rules="none">
166 <col class="field-name" />
167 <col class="field-body" />
168 <tbody valign="top">
169 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>inputs_data</strong> &#8211; dict[string, dict[string, string]]</td>
170 </tr>
171 </tbody>
172 </table>
173 </dd></dl>
174
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