Mercurial > repos > rmarenco > hubarchivecreator
annotate doc/_build/html/_modules/hubArchiveCreator.html @ 32:6d1f2bb5c1d1 draft default tip
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 5a0c39ed61b4408ba65a759aede807df260d097d
| author | yating-l |
|---|---|
| date | Sun, 26 Aug 2018 16:44:27 -0400 |
| parents | 40469b265ddb |
| children |
| rev | line source |
|---|---|
|
20
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
1 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
2 "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
3 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
4 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
5 <html xmlns="http://www.w3.org/1999/xhtml"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
6 <head> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
7 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
8 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
9 <title>hubArchiveCreator — HubArchiveCreator 2.3 documentation</title> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
10 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
11 <link rel="stylesheet" href="../_static/classic.css" type="text/css" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
12 <link rel="stylesheet" href="../_static/pygments.css" type="text/css" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
13 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
14 <script type="text/javascript"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
15 var DOCUMENTATION_OPTIONS = { |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
16 URL_ROOT: '../', |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
17 VERSION: '2.3', |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
18 COLLAPSE_INDEX: false, |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
19 FILE_SUFFIX: '.html', |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
20 HAS_SOURCE: true |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
21 }; |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
22 </script> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
23 <script type="text/javascript" src="../_static/jquery.js"></script> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
24 <script type="text/javascript" src="../_static/underscore.js"></script> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
25 <script type="text/javascript" src="../_static/doctools.js"></script> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
26 <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
27 <link rel="index" title="Index" href="../genindex.html" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
28 <link rel="search" title="Search" href="../search.html" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
29 <link rel="top" title="HubArchiveCreator 2.3 documentation" href="../index.html" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
30 <link rel="up" title="Module code" href="index.html" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
31 </head> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
32 <body role="document"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
33 <div class="related" role="navigation" aria-label="related navigation"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
34 <h3>Navigation</h3> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
35 <ul> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
36 <li class="right" style="margin-right: 10px"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
37 <a href="../genindex.html" title="General Index" |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
38 accesskey="I">index</a></li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
39 <li class="right" > |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
40 <a href="../py-modindex.html" title="Python Module Index" |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
41 >modules</a> |</li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
42 <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
43 <li class="nav-item nav-item-1"><a href="index.html" accesskey="U">Module code</a> »</li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
44 </ul> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
45 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
46 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
47 <div class="document"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
48 <div class="documentwrapper"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
49 <div class="bodywrapper"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
50 <div class="body" role="main"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
51 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
52 <h1>Source code for hubArchiveCreator</h1><div class="highlight"><pre> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
53 <span></span><span class="ch">#!/usr/bin/python</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
54 <span class="c1"># -*- coding: utf8 -*-</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
55 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
56 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
57 <span class="sd">This Galaxy tool permits to prepare your files to be ready for</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
58 <span class="sd">Assembly Hub visualization.</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
59 <span class="sd">Program test arguments:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
60 <span class="sd">hubArchiveCreator.py -g test-data/augustusDbia3.gff3 -f test-data/dbia3.fa -d . -u ./tools -o output.html</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
61 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
62 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
63 <span class="kn">import</span> <span class="nn">argparse</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
64 <span class="kn">import</span> <span class="nn">collections</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
65 <span class="kn">import</span> <span class="nn">json</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
66 <span class="kn">import</span> <span class="nn">logging</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
67 <span class="kn">import</span> <span class="nn">os</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
68 <span class="kn">import</span> <span class="nn">sys</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
69 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
70 <span class="c1"># Internal dependencies</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
71 <span class="kn">from</span> <span class="nn">Bam</span> <span class="k">import</span> <span class="n">Bam</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
72 <span class="kn">from</span> <span class="nn">BedSimpleRepeats</span> <span class="k">import</span> <span class="n">BedSimpleRepeats</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
73 <span class="kn">from</span> <span class="nn">Bed</span> <span class="k">import</span> <span class="n">Bed</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
74 <span class="kn">from</span> <span class="nn">BigWig</span> <span class="k">import</span> <span class="n">BigWig</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
75 <span class="kn">from</span> <span class="nn">util.Fasta</span> <span class="k">import</span> <span class="n">Fasta</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
76 <span class="kn">from</span> <span class="nn">util.Filters</span> <span class="k">import</span> <span class="n">TraceBackFormatter</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
77 <span class="kn">from</span> <span class="nn">Gff3</span> <span class="k">import</span> <span class="n">Gff3</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
78 <span class="kn">from</span> <span class="nn">Gtf</span> <span class="k">import</span> <span class="n">Gtf</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
79 <span class="kn">from</span> <span class="nn">Psl</span> <span class="k">import</span> <span class="n">Psl</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
80 <span class="kn">from</span> <span class="nn">TrackHub</span> <span class="k">import</span> <span class="n">TrackHub</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
81 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
82 <span class="c1"># TODO: Verify each subprocessed dependency is accessible [gff3ToGenePred, genePredToBed, twoBitInfo, faToTwoBit, bedToBigBed, sort</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
83 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
84 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
85 <span class="k">def</span> <span class="nf">main</span><span class="p">(</span><span class="n">argv</span><span class="p">):</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
86 <span class="c1"># Command Line parsing init</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
87 <span class="n">parser</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</span><span class="p">(</span><span class="n">description</span><span class="o">=</span><span class="s1">'Create a foo.txt inside the given folder.'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
88 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
89 <span class="c1"># Reference genome mandatory</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
90 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-f'</span><span class="p">,</span> <span class="s1">'--fasta'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Fasta file of the reference genome'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
91 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
92 <span class="c1"># GFF3 Management</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
93 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--gff3'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'GFF3 format'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
94 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
95 <span class="c1"># GTF Management</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
96 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--gtf'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'GTF format'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
97 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
98 <span class="c1"># Bed4+12 (TrfBig)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
99 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bedSimpleRepeats'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Bed4+12 format, using simpleRepeats.as'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
100 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
101 <span class="c1"># Generic Bed (Blastx transformed to bed)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
102 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bed'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Bed generic format'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
103 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
104 <span class="c1"># BigWig Management</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
105 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bigwig'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'BigWig format'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
106 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
107 <span class="c1"># Bam Management</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
108 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--bam'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Bam format'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
109 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
110 <span class="c1"># Psl Management</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
111 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--psl'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'append'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Psl format'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
112 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
113 <span class="c1"># TODO: Check if the running directory can have issues if we run the tool outside</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
114 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-d'</span><span class="p">,</span> <span class="s1">'--directory'</span><span class="p">,</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
115 <span class="n">help</span><span class="o">=</span><span class="s1">'Running tool directory, where to find the templates. Default is running directory'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
116 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-u'</span><span class="p">,</span> <span class="s1">'--ucsc_tools_path'</span><span class="p">,</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
117 <span class="n">help</span><span class="o">=</span><span class="s1">'Directory where to find the executables needed to run this tool'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
118 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-e'</span><span class="p">,</span> <span class="s1">'--extra_files_path'</span><span class="p">,</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
119 <span class="n">help</span><span class="o">=</span><span class="s1">'Name, in galaxy, of the output folder. Where you would want to build the Track Hub Archive'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
120 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-o'</span><span class="p">,</span> <span class="s1">'--output'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Name of the HTML summarizing the content of the Track Hub Archive'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
121 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
122 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'-j'</span><span class="p">,</span> <span class="s1">'--data_json'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Json containing the metadata of the inputs'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
123 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
124 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--user_email'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Email of the user who launched the Hub Archive Creation'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
125 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
126 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--genome_name'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'UCSC Genome Browser assembly ID'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
127 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
128 <span class="n">parser</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s1">'--debug_mode'</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="s1">'store_true'</span><span class="p">,</span> <span class="n">help</span><span class="o">=</span><span class="s1">'Allow more details about the errors'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
129 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
130 <span class="c1"># Begin init variables</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
131 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
132 <span class="n">toolDirectory</span> <span class="o">=</span> <span class="s1">'.'</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
133 <span class="n">extra_files_path</span> <span class="o">=</span> <span class="s1">'.'</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
134 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
135 <span class="c1"># Get the args passed in parameter</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
136 <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
137 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
138 <span class="n">extra_files_path</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">extra_files_path</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
139 <span class="n">toolDirectory</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">directory</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
140 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
141 <span class="c1">#### Logging management ####</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
142 <span class="c1"># If we are in Debug mode, also print in stdout the debug dump</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
143 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
144 <span class="n">configure_logger</span><span class="p">(</span><span class="n">extra_files_path</span><span class="o">=</span><span class="n">extra_files_path</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">debug_mode</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
145 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
146 <span class="c1">#### END Logging management ####</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
147 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
148 <span class="n">array_inputs_reference_genome</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">fasta</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
149 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
150 <span class="c1"># TODO: Replace these with the object Fasta</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
151 <span class="n">input_fasta_file</span> <span class="o">=</span> <span class="n">array_inputs_reference_genome</span><span class="p">[</span><span class="s2">"false_path"</span><span class="p">]</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
152 <span class="n">input_fasta_file_name</span> <span class="o">=</span> <span class="n">sanitize_name_input</span><span class="p">(</span><span class="n">array_inputs_reference_genome</span><span class="p">[</span><span class="s2">"name"</span><span class="p">])</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
153 <span class="n">genome_name</span> <span class="o">=</span> <span class="n">sanitize_name_input</span><span class="p">(</span><span class="n">args</span><span class="o">.</span><span class="n">genome_name</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
154 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
155 <span class="n">reference_genome</span> <span class="o">=</span> <span class="n">Fasta</span><span class="p">(</span><span class="n">input_fasta_file</span><span class="p">,</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
156 <span class="n">input_fasta_file_name</span><span class="p">,</span> <span class="n">genome_name</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
157 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
158 <span class="n">user_email</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">user_email</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
159 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
160 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
161 <span class="c1"># TODO: Use a class to have a better management of the structure of these inputs</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
162 <span class="c1"># These inputs are populated in the Galaxy Wrapper xml and are in this format:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
163 <span class="c1"># ARRAY[DICT{FILE_PATH: DICT{NAME: NAME_VALUE, EXTRA_DATA: EXTRA_DATA_VALUE}}]</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
164 <span class="c1"># EXTRA_DATA could be anything, for example the index of a BAM => {"index", FILE_PATH}</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
165 <span class="n">array_inputs_bam</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bam</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
166 <span class="n">array_inputs_bed_generic</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bed</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
167 <span class="n">array_inputs_bed_simple_repeats</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bedSimpleRepeats</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
168 <span class="n">array_inputs_bigwig</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">bigwig</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
169 <span class="n">array_inputs_gff3</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">gff3</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
170 <span class="n">array_inputs_gtf</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">gtf</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
171 <span class="n">array_inputs_psl</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">psl</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
172 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
173 <span class="n">outputFile</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">output</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
174 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
175 <span class="n">json_inputs_data</span> <span class="o">=</span> <span class="n">args</span><span class="o">.</span><span class="n">data_json</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
176 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
177 <span class="n">inputs_data</span> <span class="o">=</span> <span class="n">json</span><span class="o">.</span><span class="n">loads</span><span class="p">(</span><span class="n">json_inputs_data</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
178 <span class="c1"># We remove the spaces in ["name"] of inputs_data</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
179 <span class="n">sanitize_name_inputs</span><span class="p">(</span><span class="n">inputs_data</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
180 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
181 <span class="c1"># TODO: Check here all the binaries / tools we need. Exception if missing</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
182 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
183 <span class="c1"># Create the Track Hub folder</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
184 <span class="n">trackHub</span> <span class="o">=</span> <span class="n">TrackHub</span><span class="p">(</span><span class="n">reference_genome</span><span class="p">,</span> <span class="n">user_email</span><span class="p">,</span> <span class="n">outputFile</span><span class="p">,</span> <span class="n">extra_files_path</span><span class="p">,</span> <span class="n">toolDirectory</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
185 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
186 <span class="n">all_datatype_dictionary</span> <span class="o">=</span> <span class="p">{}</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
187 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
188 <span class="k">for</span> <span class="p">(</span><span class="n">inputs</span><span class="p">,</span> <span class="n">datatype_class</span><span class="p">)</span> <span class="ow">in</span> <span class="p">[</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
189 <span class="p">(</span><span class="n">array_inputs_bam</span><span class="p">,</span> <span class="n">Bam</span><span class="p">),</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
190 <span class="p">(</span><span class="n">array_inputs_bed_generic</span><span class="p">,</span> <span class="n">Bed</span><span class="p">),</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
191 <span class="p">(</span><span class="n">array_inputs_bigwig</span><span class="p">,</span> <span class="n">BigWig</span><span class="p">),</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
192 <span class="p">(</span><span class="n">array_inputs_bed_simple_repeats</span><span class="p">,</span> <span class="n">BedSimpleRepeats</span><span class="p">),</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
193 <span class="p">(</span><span class="n">array_inputs_gff3</span><span class="p">,</span> <span class="n">Gff3</span><span class="p">),</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
194 <span class="p">(</span><span class="n">array_inputs_gtf</span><span class="p">,</span> <span class="n">Gtf</span><span class="p">),</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
195 <span class="p">(</span><span class="n">array_inputs_psl</span><span class="p">,</span> <span class="n">Psl</span><span class="p">)]:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
196 <span class="k">if</span> <span class="n">inputs</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
197 <span class="n">all_datatype_dictionary</span><span class="o">.</span><span class="n">update</span><span class="p">(</span><span class="n">create_ordered_datatype_objects</span><span class="p">(</span><span class="n">datatype_class</span><span class="p">,</span> <span class="n">inputs</span><span class="p">,</span> <span class="n">inputs_data</span><span class="p">))</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
198 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
199 <span class="c1"># Create Ordered Dictionary to add the tracks in the tool form order</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
200 <span class="n">all_datatype_ordered_dictionary</span> <span class="o">=</span> <span class="n">collections</span><span class="o">.</span><span class="n">OrderedDict</span><span class="p">(</span><span class="n">all_datatype_dictionary</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
201 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
202 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"----- End of all_datatype_dictionary processing -----"</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
203 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"all_datatype_ordered_dictionary keys are: </span><span class="si">{0}</span><span class="s2">"</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">all_datatype_ordered_dictionary</span><span class="o">.</span><span class="n">values</span><span class="p">()))</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
204 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
205 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"----- Beginning of Track adding processing -----"</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
206 <span class="k">for</span> <span class="n">index</span><span class="p">,</span> <span class="n">datatypeObject</span> <span class="ow">in</span> <span class="n">all_datatype_ordered_dictionary</span><span class="o">.</span><span class="n">iteritems</span><span class="p">():</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
207 <span class="n">trackHub</span><span class="o">.</span><span class="n">addTrack</span><span class="p">(</span><span class="n">datatypeObject</span><span class="o">.</span><span class="n">track</span><span class="o">.</span><span class="n">trackDb</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
208 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"----- End of Track adding processing -----"</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
209 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
210 <span class="c1"># We process all the modifications to create the zip file</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
211 <span class="c1">#trackHub.createZip()</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
212 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
213 <span class="c1"># We terminate le process and so create a HTML file summarizing all the files</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
214 <span class="n">trackHub</span><span class="o">.</span><span class="n">terminate</span><span class="p">()</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
215 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
216 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s1">'#### End of HubArchiveCreator Debug Mode: Bye! ####'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
217 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
218 <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
219 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
220 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
221 <div class="viewcode-block" id="sanitize_name_input"><a class="viewcode-back" href="../code.html#hubArchiveCreator.sanitize_name_input">[docs]</a><span class="k">def</span> <span class="nf">sanitize_name_input</span><span class="p">(</span><span class="n">string_to_sanitize</span><span class="p">):</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
222 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
223 <span class="sd"> Sanitize the string passed in parameter by replacing '/' and ' ' by '_'</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
224 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
225 <span class="sd"> :param string_to_sanitize:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
226 <span class="sd"> :return :</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
227 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
228 <span class="sd"> :Example:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
229 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
230 <span class="sd"> >>> sanitize_name_input('this/is an//example')</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
231 <span class="sd"> this_is_an__example</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
232 <span class="sd"> """</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
233 <span class="k">return</span> <span class="n">string_to_sanitize</span> \ |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
234 <span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">"/"</span><span class="p">,</span> <span class="s2">"_"</span><span class="p">)</span> \ |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
235 <span class="o">.</span><span class="n">replace</span><span class="p">(</span><span class="s2">" "</span><span class="p">,</span> <span class="s2">"_"</span><span class="p">)</span></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
236 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
237 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
238 <div class="viewcode-block" id="sanitize_name_inputs"><a class="viewcode-back" href="../code.html#hubArchiveCreator.sanitize_name_inputs">[docs]</a><span class="k">def</span> <span class="nf">sanitize_name_inputs</span><span class="p">(</span><span class="n">inputs_data</span><span class="p">):</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
239 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
240 <span class="sd"> Sanitize value of the keys "name" of the dictionary passed in parameter.</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
241 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
242 <span class="sd"> Because sometimes output from Galaxy, or even just file name, from user inputs, have spaces.</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
243 <span class="sd"> Also, it can contain '/' character and could break the use of os.path function.</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
244 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
245 <span class="sd"> :param inputs_data: dict[string, dict[string, string]]</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
246 <span class="sd"> """</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
247 <span class="k">for</span> <span class="n">key</span> <span class="ow">in</span> <span class="n">inputs_data</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
248 <span class="n">inputs_data</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s2">"name"</span><span class="p">]</span> <span class="o">=</span> <span class="n">sanitize_name_input</span><span class="p">(</span><span class="n">inputs_data</span><span class="p">[</span><span class="n">key</span><span class="p">][</span><span class="s2">"name"</span><span class="p">])</span></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
249 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
250 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
251 <div class="viewcode-block" id="create_ordered_datatype_objects"><a class="viewcode-back" href="../code.html#hubArchiveCreator.create_ordered_datatype_objects">[docs]</a><span class="k">def</span> <span class="nf">create_ordered_datatype_objects</span><span class="p">(</span><span class="n">ExtensionClass</span><span class="p">,</span> <span class="n">array_inputs</span><span class="p">,</span> <span class="n">inputs_data</span><span class="p">):</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
252 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
253 <span class="sd"> Function which executes the creation all the necessary files / folders for a special Datatype, for TrackHub</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
254 <span class="sd"> and update the dictionary of datatype</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
255 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
256 <span class="sd"> :param ExtensionClass:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
257 <span class="sd"> :param array_inputs:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
258 <span class="sd"> :param inputs_data:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
259 <span class="sd"> :type ExtensionClass: Datatype</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
260 <span class="sd"> :type array_inputs: list[string]</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
261 <span class="sd"> :type inputs_data: dict</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
262 <span class="sd"> :rtype: dict</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
263 <span class="sd"> """</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
264 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
265 <span class="n">datatype_dictionary</span> <span class="o">=</span> <span class="p">{}</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
266 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
267 <span class="c1"># TODO: Optimize this double loop</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
268 <span class="k">for</span> <span class="n">input_false_path</span> <span class="ow">in</span> <span class="n">array_inputs</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
269 <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">data_value</span> <span class="ow">in</span> <span class="n">inputs_data</span><span class="o">.</span><span class="n">items</span><span class="p">():</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
270 <span class="k">if</span> <span class="n">key</span> <span class="o">==</span> <span class="n">input_false_path</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
271 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"input_false_path: "</span> <span class="o">+</span> <span class="n">input_false_path</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
272 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s2">"data_value: "</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">data_value</span><span class="p">))</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
273 <span class="n">extensionObject</span> <span class="o">=</span> <span class="n">ExtensionClass</span><span class="p">(</span><span class="n">input_false_path</span><span class="p">,</span> <span class="n">data_value</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
274 <span class="n">datatype_dictionary</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="n">data_value</span><span class="p">[</span><span class="s2">"order_index"</span><span class="p">]:</span> <span class="n">extensionObject</span><span class="p">})</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
275 <span class="k">return</span> <span class="n">datatype_dictionary</span></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
276 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
277 <span class="k">def</span> <span class="nf">configure_logger</span><span class="p">(</span><span class="n">extra_files_path</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">debug</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
278 <span class="k">if</span> <span class="ow">not</span> <span class="n">extra_files_path</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
279 <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"Extra files path is not set. Stopping the application"</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
280 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
281 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
282 <span class="c1"># All case log: log everything in a .log file</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
283 <span class="n">logger_file_name</span> <span class="o">=</span> <span class="s1">''</span><span class="o">.</span><span class="n">join</span><span class="p">([</span><span class="n">__name__</span><span class="p">,</span> <span class="s1">'.log'</span><span class="p">])</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
284 <span class="n">logging_file_path</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extra_files_path</span><span class="p">,</span> <span class="n">logger_file_name</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
285 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
286 <span class="n">logging</span><span class="o">.</span><span class="n">basicConfig</span><span class="p">(</span><span class="n">filename</span><span class="o">=</span><span class="n">logging_file_path</span><span class="p">,</span> <span class="n">level</span><span class="o">=</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
287 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
288 <span class="n">log_stdout</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
289 <span class="k">if</span> <span class="ow">not</span> <span class="n">debug</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
290 <span class="n">configure_logger_user</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
291 <span class="k">else</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
292 <span class="n">configure_logger_dev</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
293 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
294 <span class="c1"># stderr configuration</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
295 <span class="n">configure_logger_stderr</span><span class="p">()</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
296 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
297 <span class="n">logging</span><span class="o">.</span><span class="n">debug</span><span class="p">(</span><span class="s1">'#### Welcome in HubArchiveCreator Debug Mode ####</span><span class="se">\n</span><span class="s1">'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
298 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
299 <div class="viewcode-block" id="configure_logger_user"><a class="viewcode-back" href="../code.html#hubArchiveCreator.configure_logger_user">[docs]</a><span class="k">def</span> <span class="nf">configure_logger_user</span><span class="p">(</span><span class="n">log_stdout</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
300 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
301 <span class="sd"> User Logger is defined as following:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
302 <span class="sd"> - User needs to have WARN, ERROR and CRITICAL but well formatted / without traceback</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
303 <span class="sd"> in STDOUT</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
304 <span class="sd"> - Still access to full, brute and traceback for errors</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
305 <span class="sd"> in STDERR</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
306 <span class="sd"> - And further access to debug if needed</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
307 <span class="sd"> in .log</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
308 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
309 <span class="sd"> """</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
310 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
311 <span class="k">if</span> <span class="ow">not</span> <span class="n">log_stdout</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
312 <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"No log_stdout given. Stopping the application"</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
313 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
314 <span class="c1"># stdout for INFO / WARN / ERROR / CRITICAL</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
315 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">INFO</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
316 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
317 <span class="n">formatter</span> <span class="o">=</span> <span class="n">TraceBackFormatter</span><span class="p">(</span><span class="s1">'</span><span class="si">%(message)s</span><span class="s1">'</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
318 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
319 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
320 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
321 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
322 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
323 <div class="viewcode-block" id="configure_logger_dev"><a class="viewcode-back" href="../code.html#hubArchiveCreator.configure_logger_dev">[docs]</a><span class="k">def</span> <span class="nf">configure_logger_dev</span><span class="p">(</span><span class="n">log_stdout</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
324 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
325 <span class="sd"> Dev Logger is defined as following:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
326 <span class="sd"> - Dev needs to have WARN, ERROR and CRITICAL but well formatted / without traceback, in stdout</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
327 <span class="sd"> - Still access to full, brute and traceback in stderr for errors</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
328 <span class="sd"> - And further access to debug if needed</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
329 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
330 <span class="sd"> """</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
331 <span class="k">if</span> <span class="ow">not</span> <span class="n">log_stdout</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
332 <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s2">"No log_stdout given. Stopping the application"</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
333 <span class="n">log_format</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%(message)s</span><span class="s1">'</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
334 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
335 <span class="c1"># stdout and stderr and both identical for INFO / WARN / ERROR / CRITICAL</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
336 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">DEBUG</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
337 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
338 <span class="n">formatter</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="n">log_format</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
339 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
340 <span class="n">log_stdout</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
341 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
342 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_stdout</span><span class="p">)</span></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
343 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
344 <div class="viewcode-block" id="configure_logger_stderr"><a class="viewcode-back" href="../code.html#hubArchiveCreator.configure_logger_stderr">[docs]</a><span class="k">def</span> <span class="nf">configure_logger_stderr</span><span class="p">():</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
345 <span class="sd">"""</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
346 <span class="sd"> Configure what should be logged in stderr</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
347 <span class="sd"> """</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
348 <span class="n">log_error</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
349 <span class="n">log_error</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">ERROR</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
350 <span class="n">log_error_format</span> <span class="o">=</span> <span class="s1">'</span><span class="si">%(message)s</span><span class="s1">'</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
351 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
352 <span class="n">formatter_error</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="n">log_error_format</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
353 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
354 <span class="n">log_error</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">formatter_error</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
355 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
356 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">()</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">log_error</span><span class="p">)</span></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
357 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
358 <span class="k">if</span> <span class="n">__name__</span> <span class="o">==</span> <span class="s2">"__main__"</span><span class="p">:</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
359 <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="n">__name__</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
360 <span class="n">main</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">argv</span><span class="p">)</span> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
361 </pre></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
362 |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
363 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
364 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
365 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
366 <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
367 <div class="sphinxsidebarwrapper"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
368 <div id="searchbox" style="display: none" role="search"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
369 <h3>Quick search</h3> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
370 <form class="search" action="../search.html" method="get"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
371 <div><input type="text" name="q" /></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
372 <div><input type="submit" value="Go" /></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
373 <input type="hidden" name="check_keywords" value="yes" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
374 <input type="hidden" name="area" value="default" /> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
375 </form> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
376 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
377 <script type="text/javascript">$('#searchbox').show(0);</script> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
378 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
379 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
380 <div class="clearer"></div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
381 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
382 <div class="related" role="navigation" aria-label="related navigation"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
383 <h3>Navigation</h3> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
384 <ul> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
385 <li class="right" style="margin-right: 10px"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
386 <a href="../genindex.html" title="General Index" |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
387 >index</a></li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
388 <li class="right" > |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
389 <a href="../py-modindex.html" title="Python Module Index" |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
390 >modules</a> |</li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
391 <li class="nav-item nav-item-0"><a href="../index.html">HubArchiveCreator 2.3 documentation</a> »</li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
392 <li class="nav-item nav-item-1"><a href="index.html" >Module code</a> »</li> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
393 </ul> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
394 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
395 <div class="footer" role="contentinfo"> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
396 © Copyright 2016, Remi Marenco. |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
397 Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.4.8. |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
398 </div> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
399 </body> |
|
40469b265ddb
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 3af31e043f5b82636015c18e013d2f22ce6c9077-dirty
yating-l
parents:
diff
changeset
|
400 </html> |