# HG changeset patch
# User crs4
# Date 1433432044 14400
# Node ID 533b3b2a1e667c811b2fc969ed4d10316ef2ba24
# Parent  ec6f5279dc0182401b7197379e2eeeb131e8c42d
Update Orione citation. Add <citations> tag. Use package_muscle_3_8_31 from iuc.

diff -r ec6f5279dc01 -r 533b3b2a1e66 COPYING
--- a/COPYING	Wed Oct 30 07:34:04 2013 -0400
+++ b/COPYING	Thu Jun 04 11:34:04 2015 -0400
@@ -1,4 +1,4 @@
-Copyright © 2013 CRS4 Srl. http://www.crs4.it/
+Copyright © 2013-2014 CRS4 Srl. http://www.crs4.it/
 Created by:
 Massimiliano Orsini <massimiliano.orsini@crs4.it>
 Nicola Soranzo <nicola.soranzo@crs4.it>
diff -r ec6f5279dc01 -r 533b3b2a1e66 muscle.xml
--- a/muscle.xml	Wed Oct 30 07:34:04 2013 -0400
+++ b/muscle.xml	Thu Jun 04 11:34:04 2015 -0400
@@ -1,7 +1,8 @@
-<tool id="muscle" name="MUSCLE" version="0.0.10">
+<tool id="muscle" name="MUSCLE" version="0.0.11">
   <description>multiple aligner</description>
   <requirements>
     <requirement type="package" version="3.8.31">muscle</requirement>
+    <requirement type="set_environment">FASTA_MAX_SIZE</requirement>
   </requirements>
   <version_command>muscle -version</version_command>
   <command>
@@ -24,6 +25,8 @@
     <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/>
     <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
   </outputs>
+  <tests>
+  </tests>
   <help>
 **What it does**
 
@@ -31,20 +34,26 @@
 
 **License and citation**
 
-This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
+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 |Cuccuru2013|_.
-
-.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
-.. _Cuccuru2013: http://orione.crs4.it/
-
-This tool uses `MUSCLE`_, which is licensed separately. Please cite |Edgar2004|_.
+You can use this tool only if you agree to the license terms of: `MUSCLE`_.
 
 .. _MUSCLE: http://drive5.com/muscle/
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Edgar2004|_.
+
+.. |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* 30(13), 1928-1929
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
 .. |Edgar2004| replace:: Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. *Nucleic Acids Res.* 32(5), 1792-1797
 .. _Edgar2004: http://nar.oxfordjournals.org/content/32/5/1792
   </help>
+  <citations>
+    <citation type="doi">10.1093/nar/gkh340</citation>
+  </citations>
 </tool>
diff -r ec6f5279dc01 -r 533b3b2a1e66 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Oct 30 07:34:04 2013 -0400
+++ b/tool_dependencies.xml	Thu Jun 04 11:34:04 2015 -0400
@@ -1,27 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
+  <set_environment version="1.0">
+    <!-- MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool.
+Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources. -->
+    <environment_variable action="set_to" name="FASTA_MAX_SIZE">100000</environment_variable>
+  </set_environment>
   <package name="muscle" version="3.8.31">
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url" target_filename="muscle3.8.31.tar.gz">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action>
-        <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile -->
-        <action type="shell_command">sed -i 's/-static//g' src/mk</action>
-        <action type="shell_command">make -C src/</action>
-        <action type="move_file">
-          <source>src/muscle</source>
-          <destination>$INSTALL_DIR/bin</destination>
-        </action>
-        <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-        </action>
-        <action type="set_environment">
-          <environment_variable name="FASTA_MAX_SIZE" action="set_to">100000</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>
-MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool.
-Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources.
-    </readme>
+    <repository changeset_revision="8f20b47725d8" name="package_muscle_3_8_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>