| Next changeset 1:09552faff9c0 (2015-08-17) |
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COPYING taxonomy_krona_chart.xml tool_dependencies.xml |
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| diff -r 000000000000 -r bd565e1e3c5f COPYING --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/COPYING Fri Apr 11 12:48:59 2014 -0400 |
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| @@ -0,0 +1,23 @@ +Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/ +Created by: +Paolo Uva <paolo.uva@crs4.it> +Nicola Soranzo <nicola.soranzo@crs4.it> + +Permission is hereby granted, free of charge, to any person obtaining a +copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be included +in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS +OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. +IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY +CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, +TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE +SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
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| diff -r 000000000000 -r bd565e1e3c5f taxonomy_krona_chart.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/taxonomy_krona_chart.xml Fri Apr 11 12:48:59 2014 -0400 |
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| @@ -0,0 +1,48 @@ +<tool id="taxonomy_krona_chart" name="Krona pie chart" version="1.0.0"> + <description>from taxonomic profile</description> + <requirements> + <requirement type="package" version="2.4">kronatools</requirement> + </requirements> + <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command> + <command> + #if $input.ext == 'taxonomy' + ktImportGalaxy "${input}" -o "${output}" + #else + ktImportText "${input}" -o "${output}" + #end if + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Input file" help="Either a 'MetaPhlAn to Krona' result file or a taxonomy file" /> + </inputs> + <outputs> + <data format="html" name="output" label="${tool.name} on ${on_string}: HTML"/> + </outputs> + <help> +**What it does** + +This tool converts the standard result file of a metagenomic profiling in a zoomable pie chart using Krona_. +It takes as input datasets produced by *MetaPhlAn to Krona*, *Fetch taxonomic representation*, *Find lowest diagnostic rank* and *Filter taxonomy* tools. + +.. _Krona: http://sourceforge.net/p/krona/home/krona/ + +------ + +**License and citation** + +This Galaxy tool is Copyright © 2013-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _MIT license: http://opensource.org/licenses/MIT + +If you use this tool in Galaxy, please cite |Cuccuru2014|_. + +.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted +.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/04/03/bioinformatics.btu135 + +This tool uses scripts from `Krona`_, which is licensed separately. Please cite |Ondov2011|_. + +.. _Krona: http://sourceforge.net/p/krona/home/krona/ +.. |Ondov2011| replace:: Ondov, B. D., Bergman, N. H., Phillippy, A. M. (2011) Interactive metagenomic visualization in a Web browser. *BMC Bioinformatics* 12, 385 +.. _Ondov2011: http://www.biomedcentral.com/1471-2105/12/385 + </help> +</tool> |
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| diff -r 000000000000 -r bd565e1e3c5f tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Apr 11 12:48:59 2014 -0400 |
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| @@ -0,0 +1,19 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="kronatools" version="2.4"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://downloads.sourceforge.net/project/krona/KronaTools%20%28Mac%2C%20Linux%29/KronaTools-2.4.tar</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <!-- ./install.pl must be run inside $INSTALL_DIR . Moreover "change_directory" action does not work because $INSTALL_DIR is outside the defined working directory --> + <action type="shell_command">cd $INSTALL_DIR && ./install.pl --prefix=$INSTALL_DIR</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |