# HG changeset patch
# User simonalpha
# Date 1429357746 14400
# Node ID 0c762bc76a1ace3c57e3978c596142000e55be58

Uploaded

diff -r 000000000000 -r 0c762bc76a1a rapidnj.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rapidnj.xml	Sat Apr 18 07:49:06 2015 -0400
@@ -0,0 +1,43 @@
+<tool id="rapidnj" name="RapidNJ" version="2.3.0">
+    <description>phylogeny reconstruction</description>
+    <requirements>
+        <requirement type="package" version="2.3.0">rapidnj</requirement>
+    </requirements>
+    <command>rapidnj
+  #if int($bootstrap) > 0:
+    --bootstrap $bootstrap
+  #end if
+    $neg_branch
+    -t $aln_type
+    -i fa
+    -o t
+    -x "${output}"
+    -c \${GALAXY_SLOTS:-1}
+    "${input}"
+    </command>
+    <inputs>
+        <param format="fasta" help="Input isn't sanitised for alignment" label="Source FASTA Alignment" name="input" type="data" />
+        <param label="Alignment Type" name="aln_type" type="select">
+            <option value="d">DNA</option>
+            <option value="p">Protein</option>
+        </param>
+        <param label="Number of bootstrap samples" min="0" name="bootstrap" type="integer" value="0" />
+        <param checked="false" falsevalue="" label="Adjust for negative branch lengths" name="neg_branch" truevalue="-n" type="boolean" />
+    </inputs>
+    <outputs>
+        <data format="nhx" name="output" type="data" />
+    </outputs>
+    <stdio>
+        <regex match="ERROR"
+               source="both"
+               level="fatal"
+               description="Unknown error, check tool output" />
+    </stdio>
+    <help>
+RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining.
+http://birc.au.dk/Software/RapidNJ/
+  </help>
+    <citations>
+        <citation type="doi">10.1007/978-3-540-87361-7_10</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 0c762bc76a1a tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sat Apr 18 07:49:06 2015 -0400
@@ -0,0 +1,58 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool_dependency>
+    <package name="rapidnj" version="2.3.0">
+        <install version="1.0">
+            <actions_group>
+                <!-- Download the binaries for RapidNJ compatible with 64-bit OSX. -->
+                <actions os="darwin" architecture="x86_64">
+                    <action type="download_by_url">http://users-birc.au.dk/cstorm/software/rapidnj/bin-2.3.0/mac-64/rapidnj-mac-64.zip</action>
+                    <action type="move_file" rename_to="rapidnj">
+                        <source>rapidnj-mac-64</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for RapidNJ compatible with 32-bit OSX. -->
+                <actions os="darwin" architecture="i386">
+                    <action type="download_by_url">http://users-birc.au.dk/cstorm/software/rapidnj/bin-2.3.0/mac-32/rapidnj-mac-32.zip</action>
+                    <action type="move_file" rename_to="rapidnj">
+                        <source>rapidnj-mac-32</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for RapidNJ compatible with 64-bit Linux. -->
+                <actions os="linux" architecture="x86_64">
+                    <action type="download_by_url">http://users-birc.au.dk/cstorm/software/rapidnj/bin-2.3.0/linux-64/rapidnj-linux-64.zip</action>
+                    <action type="move_file" rename_to="rapidnj">
+                        <source>rapidnj-linux-64</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <!-- Download the binaries for RapidNJ compatible with 32-bit Linux. -->
+                <actions os="linux" architecture="i386">
+                    <action type="download_by_url">http://users-birc.au.dk/cstorm/software/rapidnj/bin-2.3.0/linux-32/rapidnj-linux-32.zip</action>
+                    <action type="move_file" rename_to="rapidnj">
+                        <source>rapidnj-linux-32</source>
+                        <destination>$INSTALL_DIR</destination>
+                    </action>
+                </actions>
+                <action type="chmod">
+                  <file mode="755">$INSTALL_DIR/rapidnj</file>
+                </action>
+                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X RapidNJ
+binaries, which is faster than performing a local compilation,
+avoids any issues with build dependencies, and is more reproducible between
+installations as there is no variability from the compiler or library
+versions.
+
+For more details, see:
+http://birc.au.dk/Software/RapidNJ/
+        </readme>
+    </package>
+</tool_dependency>