comparison blast2html.xml @ 0:dad02776f538

first commit

0:dad02776f538

<tool id="blast2html_test" name="blast2html_test" version="0.0.14">
    
    <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>
        
    <help>
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:: images/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


Galaxy configuration
--------------------

This tool generates an HTML page from Blast XML input. It can be used as a stand-alone command line tool, but it is meant to be used in workflows in Galaxy_. To use this tool in Galaxy some configuration may be required.

By default Galaxy strips a lot of style information from HTML files before showing them on the screen. The results of this tool will still be somewhat useful but they will be a lot uglier without the styles. You can still download the original generated HTML of course. If you want to view the full result within Galaxy you need to disable this stripping of style information by adding the following line to your Galaxy's ``galaxy.ini``::

    sanitize_all_html = False

In order to generate links to a gene bank in the result, you will need to tell blast2html what gene bank to use. If you do not configure a gene bank the result will contain links to the NCBI gene bank, and as a name for the gene bank the generic "Gene Bank" is used. These links will only work if the database you are using uses the same accession codes as the NCBI gene bank. To show links to a different gene bank this needs to be configured in Galaxy.

As at the moment this tool was built Galaxy did not have a good way to specify such configuration directives to tools, we use a slightly ugly solution. The gene bank configuration are added to the NCBI BLAST+ database definition files in Galaxy's ``tool-data`` directory. This directory should contain some files named ``blastdb.loc``, ``blastdb_p.loc``, ``blastdb_d.loc`` etc. that define the databases that the NCBI BLAST+ tool knows about. For BLAST, these files contain three columns of tab-separated data that define the databases. The normal format is::

  &lt;unique_id&gt;    &lt;database_caption&gt;      &lt;base_name_path&gt;

with tabs separating the three components. For blast2html we extend this format with two columns that contain a human-readable gene bank name, and a link template. So each row then contains these tab-separated items::

  &lt;unique_id&gt;    &lt;database_caption&gt;      &lt;base_name_path&gt;     &lt;genebank_name&gt;     &lt;genebank_link_template&gt;

NCBI Blast+ will ignore the extra fields in the file.

So, for example, for a database named ``nt`` with path ``/depot/data2/galaxy/blastdb/nt/nt.chunk`` that uses NCBI nucleontide database accession codes you can use the following definition line::

  nt_02_Dec_2009        nt 02 Dec 2009  /depot/data2/galaxy/blastdb/nt/nt.chunk NCBI Gene Bank  http://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=genbank&amp;log$=nuclalign

The syntax for the link template is the same as that used by the ``--genelink-template`` command line option (see next section):  It can contain the following replacement elements: ``{id[N]}``, ``{fullid}``, ``{defline[N]}``, ``{fulldefline}``, ``{accession}``, where ``N`` is a number. ``id[N]`` and ``defline[N]`` will be replaced by the Nth element of the id or defline, where '``|``' is the field separator.


.. _Galaxy: https://www.galaxyproject.org/


Command line usage
------------------

::

    usage: ./blast2html.py [-i] INPUT [-o OUTPUT] [--genelink-template URL_TEMPLATE] [--dbname DBNAME]

    Convert a BLAST XML result into a nicely readable html page

    positional arguments:
      INPUT                 The input Blast XML file, same as -i/--input

    optional arguments:
      -h, --help            show this help message and exit
      -i INPUT, --input INPUT
                            The input Blast XML file
      -o OUTPUT, --output OUTPUT
                            The output html file
      --template TEMPLATE   The template file to use. Defaults to
                            blast_html.html.jinja
      --dbname DBNAME       The link text to use for external links to a gene bank
                            database. Defaults to 'Gene Bank'
      --genelink-template URL_TEMPLATE
                            A link template to link hits to a gene bank webpage.
                            The template string is a Python format string. It can
                            contain the following replacement elements: {id[N]},
                            {fullid}, {defline[N]}, {fulldefline}, {accession},
                            where N is a number. id[N] and defline[N] will be
                            replaced by the Nth element of the id or defline,
                            where '|' is the field separator. The default is 'http
                            ://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report=
                            genbank&amp;log$=nuclalign', which is a link to the NCBI
                            nucleotide database.
      --db-config-dir DB_CONFIG_DIR
                            The directory where databases are configured in
                            blastdb*.loc files. These files are consulted for
                            creating a gene bank link. The files should conform to
                            the format that Galaxy's BLAST expect, i.e. tab-
                            separated tables (with lines starting with '#'
                            ignored), with two extra fields, for a total of five
                            fields per line instead of three.. The third field of
                            each line should be a database path as used by BLAST.
                            The fourth field is the human readable database name,
                            and the fifth a template link to the gene bank
                            conforming to the syntax for the --genelink-template
                            option. Entries in these config files override links
                            specified using --genelink-template and --dbname.


Authorship
----------

This tool was created and published by `The Hyve B.V.`_ open source bioinformatics solutions.

.. image:: images/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>