--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Wed Oct 30 07:34:04 2013 -0400
@@ -0,0 +1,23 @@
+Copyright © 2013 CRS4 Srl. http://www.crs4.it/
+Created by:
+Massimiliano Orsini <massimiliano.orsini@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.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/muscle.xml	Wed Oct 30 07:34:04 2013 -0400
@@ -0,0 +1,50 @@
+<tool id="muscle" name="MUSCLE" version="0.0.10">
+  <description>multiple aligner</description>
+  <requirements>
+    <requirement type="package" version="3.8.31">muscle</requirement>
+  </requirements>
+  <version_command>muscle -version</version_command>
+  <command>
+    FASTA_MAX_SIZE=\${FASTA_MAX_SIZE:-100000};
+    if [ `stat -c "%s" $multifasta` -gt \$FASTA_MAX_SIZE ]; then echo "Multi-FASTA file is bigger than the configured limit for MUSCLE (\$FASTA_MAX_SIZE bytes)." >&amp;2; exit 1; fi;
+    muscle -quiet -in $multifasta -out $output -log $log
+    #if str($maxiters)
+      -maxiters $maxiters
+    #end if
+    #if $diags
+      -diags
+    #end if
+  </command>
+  <inputs>
+    <param name="multifasta" type="data" format="fasta" label="Multi-FASTA file" />
+    <param name="maxiters" type="integer" value="2" min="1" max="16" optional="true" label="Maximum number of iterations to run (-maxiters)" help="Set to 2 for large datasets where refinement (iterations 3+) is too slow." />
+    <param name="diags" type="boolean" label="Diagonal optimization (-diags)" help="Speed up the algorithm, especially for closely related sequences, at the expense of some reduction in accuracy" />
+  </inputs>
+  <outputs>
+    <data name="output" format="fasta" label="${tool.name} on ${on_string}: aligned sequences"/>
+    <data name="log" format="txt" label="${tool.name} on ${on_string}: log"/>
+  </outputs>
+  <help>
+**What it does**
+
+This tool performs multiple sequence alignment using MUSCLE.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2013 `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|_.
+
+.. _MUSCLE: http://drive5.com/muscle/
+.. |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>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Oct 30 07:34:04 2013 -0400
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <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>
+  </package>
+</tool_dependency>