Mercurial > repos > jankanis > blast2html_test2
changeset 2:b39e07d89fda
Update help
| author | Jan Kanis <jan.code@jankanis.nl> |
|---|---|
| date | Thu, 23 Jul 2015 11:24:47 +0200 |
| parents | 9272a08cb8fe |
| children | b98111afad32 6d8238fa0cca |
| files | blast2html.xml |
| diffstat | 1 files changed, 26 insertions(+), 78 deletions(-) [+] |
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--- a/blast2html.xml Thu Jul 23 09:46:31 2015 +0200 +++ b/blast2html.xml Thu Jul 23 11:24:47 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="blast2html_test" name="blast2html_test" version="0.0.18"> +<tool id="blast2html_test" name="blast2html_test" version="0.0.19"> <description>Convert BLAST XML to HTML</description> @@ -21,8 +21,20 @@ <outputs> <data format="html" name="output" /> </outputs> - - <help> + + <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 ============================================= @@ -41,91 +53,27 @@ .. _`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:: - - <unique_id> <database_caption> <base_name_path> +Output display +-------------- -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:: - - <unique_id> <database_caption> <base_name_path> <genebank_name> <genebank_link_template> - -NCBI Blast+ will ignore the extra fields in the file. +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. -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&log$=nuclalign - -The syntax for the link template is the same as that used by the ``--genelink-template`` command line option (see next section): It can contain the following replacement elements: ``{id[N]}``, ``{fullid}``, ``{defline[N]}``, ``{fulldefline}``, ``{accession}``, where ``N`` is a number. ``id[N]`` and ``defline[N]`` will be replaced by the Nth element of the id or defline, where '``|``' is the field separator. - - -.. _Galaxy: https://www.galaxyproject.org/ +To remove this warning, a Galaxy administrator needs to set the ``sanitize_all_html`` to ``false`` in the Galaxy configuration. -Command line usage ------------------- - -:: - - usage: ./blast2html.py [-i] INPUT [-o OUTPUT] [--genelink-template URL_TEMPLATE] [--dbname DBNAME] - - Convert a BLAST XML result into a nicely readable html page - - positional arguments: - INPUT The input Blast XML file, same as -i/--input +Genebank links +-------------- - optional arguments: - -h, --help show this help message and exit - -i INPUT, --input INPUT - The input Blast XML file - -o OUTPUT, --output OUTPUT - The output html file - --template TEMPLATE The template file to use. Defaults to - blast_html.html.jinja - --dbname DBNAME The link text to use for external links to a gene bank - database. Defaults to 'Gene Bank' - --genelink-template URL_TEMPLATE - A link template to link hits to a gene bank webpage. - The template string is a Python format string. It can - contain the following replacement elements: {id[N]}, - {fullid}, {defline[N]}, {fulldefline}, {accession}, - where N is a number. id[N] and defline[N] will be - replaced by the Nth element of the id or defline, - where '|' is the field separator. The default is 'http - ://www.ncbi.nlm.nih.gov/nucleotide/{accession}?report= - genbank&log$=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. +If the links to gene banks are not working correctly, the Galaxy administrator needs to configure them. See this tools README file for details. -Authorship ----------- +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