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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1a81ebd0ddea950b84af3fc830e9267a4814b29f
author yating-l
date Mon, 06 Nov 2017 13:13:01 -0500
parents 4ced8f116509
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1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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2 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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5 <html xmlns="http://www.w3.org/1999/xhtml">
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6 <head>
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7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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9 <title>Auto Generated Documentation &#8212; HubArchiveCreator 2.3 documentation</title>
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10
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11 <link rel="stylesheet" href="_static/classic.css" type="text/css" />
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12 <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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13
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14 <script type="text/javascript">
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15 var DOCUMENTATION_OPTIONS = {
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16 URL_ROOT: './',
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17 VERSION: '2.3',
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18 COLLAPSE_INDEX: false,
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19 FILE_SUFFIX: '.html',
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20 HAS_SOURCE: true
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21 };
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22 </script>
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23 <script type="text/javascript" src="_static/jquery.js"></script>
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24 <script type="text/javascript" src="_static/underscore.js"></script>
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25 <script type="text/javascript" src="_static/doctools.js"></script>
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26 <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
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27 <link rel="index" title="Index" href="genindex.html" />
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28 <link rel="search" title="Search" href="search.html" />
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29 <link rel="top" title="HubArchiveCreator 2.3 documentation" href="index.html" />
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30 <link rel="prev" title="Welcome to HubArchiveCreator’s documentation!" href="index.html" />
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31 </head>
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32 <body role="document">
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33 <div class="related" role="navigation" aria-label="related navigation">
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34 <h3>Navigation</h3>
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35 <ul>
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36 <li class="right" style="margin-right: 10px">
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37 <a href="genindex.html" title="General Index"
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38 accesskey="I">index</a></li>
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39 <li class="right" >
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40 <a href="py-modindex.html" title="Python Module Index"
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41 >modules</a> |</li>
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42 <li class="right" >
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43 <a href="index.html" title="Welcome to HubArchiveCreator’s documentation!"
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44 accesskey="P">previous</a> |</li>
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45 <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> &#187;</li>
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46 </ul>
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47 </div>
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48
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49 <div class="document">
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50 <div class="documentwrapper">
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51 <div class="bodywrapper">
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52 <div class="body" role="main">
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53
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54 <div class="section" id="module-hubArchiveCreator">
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55 <span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-hubArchiveCreator" title="Permalink to this headline">¶</a></h1>
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56 <p>This Galaxy tool permits to prepare your files to be ready for
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57 Assembly Hub visualization.
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58 Program test arguments:
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59 hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</p>
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60 <dl class="function">
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61 <dt id="hubArchiveCreator.configure_logger_dev">
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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>
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63 <dd><dl class="docutils">
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64 <dt>Dev Logger is defined as following:</dt>
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65 <dd><ul class="first last simple">
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66 <li>Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout</li>
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67 <li>Still access to full, brute and traceback in stderr for errors</li>
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68 <li>And further access to debug if needed</li>
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69 </ul>
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70 </dd>
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71 </dl>
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72 </dd></dl>
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73
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74 <dl class="function">
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75 <dt id="hubArchiveCreator.configure_logger_stderr">
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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>
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77 <dd><p>Configure what should be logged in stderr</p>
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78 </dd></dl>
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79
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80 <dl class="function">
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81 <dt id="hubArchiveCreator.configure_logger_user">
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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>
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83 <dd><dl class="docutils">
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84 <dt>User Logger is defined as following:</dt>
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85 <dd><ul class="first last">
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86 <li><dl class="first docutils">
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87 <dt>User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback</dt>
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88 <dd><p class="first last">in STDOUT</p>
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89 </dd>
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90 </dl>
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91 </li>
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92 <li><dl class="first docutils">
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93 <dt>Still access to full, brute and traceback for errors</dt>
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94 <dd><p class="first last">in STDERR</p>
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95 </dd>
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96 </dl>
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97 </li>
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98 <li><dl class="first docutils">
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99 <dt>And further access to debug if needed</dt>
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100 <dd><p class="first last">in .log</p>
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101 </dd>
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102 </dl>
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103 </li>
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104 </ul>
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105 </dd>
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106 </dl>
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107 </dd></dl>
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108
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109 <dl class="function">
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110 <dt id="hubArchiveCreator.create_ordered_datatype_objects">
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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>
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112 <dd><p>Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub
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113 and update the dictionary of datatype</p>
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114 <table class="docutils field-list" frame="void" rules="none">
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115 <col class="field-name" />
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116 <col class="field-body" />
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117 <tbody valign="top">
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118 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
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119 <li><strong>ExtensionClass</strong> (<em>Datatype</em>) &#8211; </li>
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120 <li><strong>array_inputs</strong> (<em>list[string]</em>) &#8211; </li>
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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>
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122 </ul>
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123 </td>
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124 </tr>
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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>
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126 </td>
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127 </tr>
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128 </tbody>
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129 </table>
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130 </dd></dl>
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131
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132 <dl class="function">
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133 <dt id="hubArchiveCreator.sanitize_name_input">
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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>
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135 <dd><p>Sanitize the string passed in parameter by replacing &#8216;/&#8217; and &#8216; &#8216; by &#8216;_&#8217;</p>
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136 <table class="docutils field-list" frame="void" rules="none">
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137 <col class="field-name" />
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138 <col class="field-body" />
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139 <tbody valign="top">
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140 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>string_to_sanitize</strong> &#8211; </td>
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141 </tr>
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142 </tbody>
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143 </table>
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144 <p>:return :</p>
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145 <table class="docutils field-list" frame="void" rules="none">
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146 <col class="field-name" />
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147 <col class="field-body" />
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148 <tbody valign="top">
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149 <tr class="field-odd field"><th class="field-name">Example:</th><td class="field-body"></td>
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150 </tr>
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151 </tbody>
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152 </table>
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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>
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154 <span class="go">this_is_an__example</span>
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155 </pre></div>
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156 </div>
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157 </dd></dl>
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158
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159 <dl class="function">
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160 <dt id="hubArchiveCreator.sanitize_name_inputs">
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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>
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162 <dd><p>Sanitize value of the keys &#8220;name&#8221; of the dictionary passed in parameter.</p>
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163 <p>Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.
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164 Also, it can contain &#8216;/&#8217; character and could break the use of os.path function.</p>
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165 <table class="docutils field-list" frame="void" rules="none">
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166 <col class="field-name" />
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167 <col class="field-body" />
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168 <tbody valign="top">
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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>
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170 </tr>
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171 </tbody>
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172 </table>
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173 </dd></dl>
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174
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175 </div>
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176
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177
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178 </div>
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179 </div>
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180 </div>
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181 <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
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182 <div class="sphinxsidebarwrapper">
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183 <h4>Previous topic</h4>
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184 <p class="topless"><a href="index.html"
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185 title="previous chapter">Welcome to HubArchiveCreator&#8217;s documentation!</a></p>
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186 <div role="note" aria-label="source link">
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187 <h3>This Page</h3>
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188 <ul class="this-page-menu">
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189 <li><a href="_sources/code.txt"
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190 rel="nofollow">Show Source</a></li>
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191 </ul>
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192 </div>
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193 <div id="searchbox" style="display: none" role="search">
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194 <h3>Quick search</h3>
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195 <form class="search" action="search.html" method="get">
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196 <div><input type="text" name="q" /></div>
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197 <div><input type="submit" value="Go" /></div>
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198 <input type="hidden" name="check_keywords" value="yes" />
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199 <input type="hidden" name="area" value="default" />
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200 </form>
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201 </div>
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202 <script type="text/javascript">$('#searchbox').show(0);</script>
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203 </div>
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204 </div>
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205 <div class="clearer"></div>
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206 </div>
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207 <div class="related" role="navigation" aria-label="related navigation">
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208 <h3>Navigation</h3>
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209 <ul>
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210 <li class="right" style="margin-right: 10px">
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211 <a href="genindex.html" title="General Index"
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212 >index</a></li>
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213 <li class="right" >
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214 <a href="py-modindex.html" title="Python Module Index"
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215 >modules</a> |</li>
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216 <li class="right" >
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217 <a href="index.html" title="Welcome to HubArchiveCreator’s documentation!"
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218 >previous</a> |</li>
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219 <li class="nav-item nav-item-0"><a href="index.html">HubArchiveCreator 2.3 documentation</a> &#187;</li>
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220 </ul>
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221 </div>
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222 <div class="footer" role="contentinfo">
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223 &#169; Copyright 2016, Remi Marenco.
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224 Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8.
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225 </div>
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226 </body>
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227 </html>