changeset 0:bd565e1e3c5f draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Fri Apr 11 12:48:59 2014 -0400
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+Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/
+Created by:
+Paolo Uva <[e-mail]>
+Nicola Soranzo <[e-mail]>
+
+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.

--- /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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+<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>

--- /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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+<?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 $INSTALL_DIR &amp;&amp; ./install.pl --prefix=$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>