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Version 1.0: Include documentation, license, etc. No code changes Update README, put appropriate text in the <help> section, add a <citation> tag.
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 23 Jul 2015 12:08:51 +0200
parents 8ae714069687
children
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126:0fa962dd83b4 127:532aa200dbe9
1 <tool id="blast2html" name="blast2html" version="0.0.14"> 1 <tool id="blast2html" name="blast2html" version="1.0.0">
2 2
3 <description>Convert BLAST XML to HTML</description> 3 <description>Convert BLAST XML to HTML</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement name="package" version="0.2">blast2html_venv</requirement> 6 <requirement name="package" version="0.2">blast2html_venv</requirement>
39 <param name="input" value="blast xml example4.xml"/> 39 <param name="input" value="blast xml example4.xml"/>
40 <output name="output" file="blast xml example4.html"/> 40 <output name="output" file="blast xml example4.html"/>
41 </test> 41 </test>
42 </tests> 42 </tests>
43 43
44 <help> 44 <citation>
45 This tool converts the default BLAST XML result into a HTML document 45 <citation type="bibtex">
46 @misc{Blast2html,
47 author = "Jan Kanis",
48 title = "Blast2html: A tool to display Blast XML as HTML",
49 howpublished = "Available on the Toolshed website for the Galaxy Project, https://toolshed.g2.bx.psu.edu/repository?repository_id=f32220daa6f46e04",
50 year = "2015",
51 note = "Created by The Hyve Open Source Bioinformatics Solutions, http://thehyve.nl"
52 }
53 </citation>
54 </citation>
55
56 <help><!-- The contents of this is displayed in galaxy once installed. Format is rst. -->
57 Blast2html: Blast XML to HTML conversion tool
58 =============================================
59
60 This tool accepts Blast XML as input, and creates an HTML page with a human readable version of the result. The output includes graphical displays of where a sequence matches a target and metrics on the quality of the match.
61
62 Example output:
63
64 .. image:: blast2html_screenshot1.png
65 :alt: Screenshot of sample output
66 :align: center
67
68 The output format is based on the graphical summary pages on the `NCBI Blast website`_. But as the code for generating such pages is not available we implemented our own clone.
69
70 .. _`NCBI Blast website`: http://blast.ncbi.nlm.nih.gov/Blast.cgi
71
72
73 Output display
74 --------------
75
76 If, when viewing the output, you see a warning that Galaxy has stripped the html page, that means Galaxy is not displaying the full html page in the layout that it is supposed to have. Most of the information is still visible in a less pleasing layout. To access the full result page, you will need to download the result and view it on your own computer.
77
78 To remove this warning, a Galaxy administrator needs to set the ``sanitize_all_html`` to ``false`` in the Galaxy configuration.
79
80
81 Genebank links
82 --------------
83
84 If the links to gene banks are not working correctly, the Galaxy administrator needs to configure them. See this tools README file for details.
85
86
87 Citations
88 ---------
89
90 This tool was created and published by `The Hyve B.V.`_ Open Source Bioinformatics Solutions.
91
92 If you publish anything for which you make use of this tool, please be so kind to mention that in the publication.
93
94 .. image:: thehyve_logo.png
95 :alt: The Hyve
96 :align: center
97 :target: http://thehyve.nl
98
99 .. _`The Hyve B.V.`: http://thehyve.nl/
100
101
102 Licensing information
103 ---------------------
104
105 Blast2html is free software: you can redistribute it and/or modify
106 it under the terms of the GNU General Public License as published by
107 the Free Software Foundation, either version 3 of the License, or
108 (at your option) any later version.
109
110 This program is distributed in the hope that it will be useful,
111 but WITHOUT ANY WARRANTY; without even the implied warranty of
112 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
113 GNU General Public License for more details.
114
115 You should have received a copy of the GNU General Public License
116 along with this program. If not, see &lt;http://www.gnu.org/licenses/&gt;.
46 </help> 117 </help>
47 118
48 </tool> 119 </tool>