annotate blast2html.xml @ 128:82b8c9722996 default tip

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<tool id="blast2html" name="blast2html" version="1.0.0">
    
    <description>Convert BLAST XML to HTML</description>
    
    <requirements>
      <requirement name="package" version="0.2">blast2html_venv</requirement>
    </requirements>
    
    <command interpreter="python">blast2html.py -i "${input}" -o "${output}" --db-config-dir "${GALAXY_DATA_INDEX_DIR}"</command>

    <stdio>
      <!-- Any exit code other than 0 is an error -->
      <exit_code range="1:" />
      <exit_code range=":-1" />
    </stdio>
    
    <inputs>
        <param format="blastxml" name="input" type="data" label="Source file"/>
    </inputs>
    
    <outputs>
        <data format="html" name="output" />
    </outputs>
    
    <tests>
        <test>
            <param name="input" value="blast xml example1.xml"/>
            <output name="output" file="blast xml example1.html"/>
        </test>
        <test>
            <param name="input" value="blast xml example2.xml"/>
            <output name="output" file="blast xml example2.html"/>
        </test>
        <test>
            <param name="input" value="blast xml example3.xml"/>
            <output name="output" file="blast xml example3.html"/>
        </test>
        <test>
            <param name="input" value="blast xml example4.xml"/>
            <output name="output" file="blast xml example4.html"/>
        </test>
    </tests>
    
    <citation>
      <citation type="bibtex">
	@misc{Blast2html,
	 author = "Jan Kanis",
	 title = "Blast2html: A tool to display Blast XML as HTML",
	 howpublished = "Available on the Toolshed website for the Galaxy Project, https://toolshed.g2.bx.psu.edu/repository?repository_id=f32220daa6f46e04",
	 year = "2015",
	 note = "Created by The Hyve Open Source Bioinformatics Solutions, http://thehyve.nl"
	}
      </citation>
    </citation>
    
    <help><!-- The contents of this is displayed in galaxy once installed. Format is rst. -->
Blast2html: Blast XML to HTML conversion tool
=============================================

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.

Example output:

.. image:: blast2html_screenshot1.png
    :alt: Screenshot of sample output
    :align: center

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. 

.. _`NCBI Blast website`: http://blast.ncbi.nlm.nih.gov/Blast.cgi


Output display
--------------

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.

To remove this warning, a Galaxy administrator needs to set the ``sanitize_all_html`` to ``false`` in the Galaxy configuration.


Genebank links
--------------

If the links to gene banks are not working correctly, the Galaxy administrator needs to configure them. See this tools README file for details.


Citations
---------

This tool was created and published by `The Hyve B.V.`_ Open Source Bioinformatics Solutions.

If you publish anything for which you make use of this tool, please be so kind to mention that in the publication.

.. image:: thehyve_logo.png
    :alt: The Hyve
    :align: center
    :target: http://thehyve.nl

.. _`The Hyve B.V.`: http://thehyve.nl/


Licensing information
---------------------

Blast2html is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.
    </help>
    
</tool>