--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jan 27 09:06:06 2015 -0500
@@ -0,0 +1,65 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="perl" version="5.18.1">
+      <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="0.12.7">
+      <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="mirdeep2_mapper" version="2.0">
+      <install version="1.0">
+          <actions>
+              <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action>
+                <action type="move_file">
+                  <source>clip_adapters.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>collapse_reads_md.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>convert_bowtie_output.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>fastaparse.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>fastq2fasta.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>illumina_to_fasta.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>mapper.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>parse_mappings.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="move_file">
+                  <source>rna2dna.pl</source>
+                    <destination>$INSTALL_DIR</destination>
+                </action>
+                <action type="set_environment">
+                  <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+
+Processes reads and/or maps them to the reference genome.
+
+input:
+Default input is a file in fasta, seq.txt or qseq.txt format. More input can be given depending on the options used.
+output:
+The output depends on the options used (see below). Either a fasta file with processed reads or an arf file with with mapped reads, or both, are output. 
+
+        </readme>
+    </package>
+</tool_dependency>