blast2html: blast2html.xml annotate

annotate blast2html.xml @ 128:82b8c9722996 default tip

Add links to github and bitbucket

author	Jan Kanis <jan.code@jankanis.nl>
date	Thu, 23 Jul 2015 12:24:40 +0200
parents	532aa200dbe9
children

rev	line source
127 532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	1 <tool id="blast2html" name="blast2html" version="1.0.0">
28 8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	2
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	3 <description>Convert BLAST XML to HTML</description>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	4
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	5 <requirements>
85 2edb77030a9e re-include backed out revisions and update version numbers Jan Kanis <jan.code@jankanis.nl> parents: 84 diff changeset	6 <requirement name="package" version="0.2">blast2html_venv</requirement>
28 8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	7 </requirements>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	8
100 be7c94e29cd8 add --db-config-dir switch to wrapper; update version number Jan Kanis <jan.code@jankanis.nl> parents: 85 diff changeset	9 <command interpreter="python">blast2html.py -i "${input}" -o "${output}" --db-config-dir "${GALAXY_DATA_INDEX_DIR}"</command>
38 91008923c402 add repository dependency; add <stdio> tag; update version Jan Kanis <jan.code@jankanis.nl> parents: 37 diff changeset	10
91008923c402 add repository dependency; add <stdio> tag; update version Jan Kanis <jan.code@jankanis.nl> parents: 37 diff changeset	11 <stdio>
91008923c402 add repository dependency; add <stdio> tag; update version Jan Kanis <jan.code@jankanis.nl> parents: 37 diff changeset	12 <!-- Any exit code other than 0 is an error -->
91008923c402 add repository dependency; add <stdio> tag; update version Jan Kanis <jan.code@jankanis.nl> parents: 37 diff changeset	13 <exit_code range="1:" />
91008923c402 add repository dependency; add <stdio> tag; update version Jan Kanis <jan.code@jankanis.nl> parents: 37 diff changeset	14 <exit_code range=":-1" />
91008923c402 add repository dependency; add <stdio> tag; update version Jan Kanis <jan.code@jankanis.nl> parents: 37 diff changeset	15 </stdio>
28 8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	16
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	17 <inputs>
66 e3dd39906eef fix input format Jan Kanis <jan.code@jankanis.nl> parents: 61 diff changeset	18 <param format="blastxml" name="input" type="data" label="Source file"/>
28 8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	19 </inputs>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	20
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	21 <outputs>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	22 <data format="html" name="output" />
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	23 </outputs>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	24
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	25 <tests>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	26 <test>
32 ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	27 <param name="input" value="blast xml example1.xml"/>
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 100 diff changeset	28 <output name="output" file="blast xml example1.html"/>
28 8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	29 </test>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	30 <test>
32 ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	31 <param name="input" value="blast xml example2.xml"/>
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 100 diff changeset	32 <output name="output" file="blast xml example2.html"/>
32 ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	33 </test>
ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	34 <test>
ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	35 <param name="input" value="blast xml example3.xml"/>
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 100 diff changeset	36 <output name="output" file="blast xml example3.html"/>
32 ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	37 </test>
ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	38 <test>
ce8f29efc0a1 fix tests Jan Kanis <jan.code@jankanis.nl> parents: 29 diff changeset	39 <param name="input" value="blast xml example4.xml"/>
105 b3b5ee557170 update test Jan Kanis <jan.code@jankanis.nl> parents: 100 diff changeset	40 <output name="output" file="blast xml example4.html"/>
28 8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	41 </test>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	42 </tests>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	43
127 532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	44 <citation>
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	45 <citation type="bibtex">
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	46 @misc{Blast2html,
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	47 author = "Jan Kanis",
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	48 title = "Blast2html: A tool to display Blast XML as HTML",
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	49 howpublished = "Available on the Toolshed website for the Galaxy Project, https://toolshed.g2.bx.psu.edu/repository?repository_id=f32220daa6f46e04",
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	50 year = "2015",
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	51 note = "Created by The Hyve Open Source Bioinformatics Solutions, http://thehyve.nl"
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	52 }
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	53 </citation>
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	54 </citation>
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	55
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	56 <help><!-- The contents of this is displayed in galaxy once installed. Format is rst. -->
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	57 Blast2html: Blast XML to HTML conversion tool
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	58 =============================================
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	59
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	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.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	61
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	62 Example output:
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	63
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	64 .. image:: blast2html_screenshot1.png
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	65 :alt: Screenshot of sample output
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	66 :align: center
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	67
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	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.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	69
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	70 .. _`NCBI Blast website`: http://blast.ncbi.nlm.nih.gov/Blast.cgi
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	71
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	72
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	73 Output display
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	74 --------------
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	75
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	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.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	77
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	78 To remove this warning, a Galaxy administrator needs to set the ``sanitize_all_html`` to ``false`` in the Galaxy configuration.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	79
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	80
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	81 Genebank links
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	82 --------------
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	83
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	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.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	85
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	86
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	87 Citations
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	88 ---------
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	89
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	90 This tool was created and published by `The Hyve B.V.`_ Open Source Bioinformatics Solutions.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	91
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	92 If you publish anything for which you make use of this tool, please be so kind to mention that in the publication.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	93
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	94 .. image:: thehyve_logo.png
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	95 :alt: The Hyve
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	96 :align: center
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	97 :target: http://thehyve.nl
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	98
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	99 .. _`The Hyve B.V.`: http://thehyve.nl/
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	100
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	101
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	102 Licensing information
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	103 ---------------------
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	104
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	105 Blast2html is free software: you can redistribute it and/or modify
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	106 it under the terms of the GNU General Public License as published by
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	107 the Free Software Foundation, either version 3 of the License, or
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	108 (at your option) any later version.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	109
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	110 This program is distributed in the hope that it will be useful,
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	111 but WITHOUT ANY WARRANTY; without even the implied warranty of
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	112 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	113 GNU General Public License for more details.
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	114
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	115 You should have received a copy of the GNU General Public License
532aa200dbe9 Version 1.0: Include documentation, license, etc. No code changes Jan Kanis <jan.code@jankanis.nl> parents: 117 diff changeset	116 along with this program. If not, see <http://www.gnu.org/licenses/>.
28 8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	117 </help>
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	118
8a8c0c71b5d1 add blast2html.xml config setting Jan Kanis <jan.code@jankanis.nl> parents: diff changeset	119 </tool>

Mercurial > repos > jankanis > blast2html

annotate blast2html.xml @ 128:82b8c9722996 default tip