--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Oct 15 13:24:55 2015 -0400
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="python" version="2.7.10">
+        <repository changeset_revision="4f81728216e7" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="pathoscope" version="2.0.6">
+        <install version="1.0">
+            <actions>
+                <action type="setup_python_environment">
+                    <repository changeset_revision="4f81728216e7" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="python" version="2.7.10" />
+                    </repository>
+                    <package>https://github.com/PathoScope/PathoScope/archive/v2.0.6.zip</package>
+                </action>
+                <action type="set_environment">
+                    <environment_variable action="set_to" name="PYTHONPATH_PATHOSCOPE">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            Pathoscope 2.0 consists of four core and two optional analysis modules
+            for sequencing-based metagenomic profiling. The PathoLib module
+            extracts genome reference libraries (target or host/filter) from all
+            available sequences in the NCBI Nucleotide database that belong to a
+            user-defined taxonomic clade. The PathoMap module aligns the reads to
+            the target reference library and removes any reads that have sequence
+            similarity with the host or filter genomes. PathoID resolves read
+            ambiguity, identifies which of the target genomes are present in the
+            sample and estimates the proportions of reads originating from each
+            genome. PathoReport provides two report files: 1) a summary report
+            (.tsv) that contains the numbers and proportions of reads aligned to
+            each genome identified in the sample, and 2) detailed report (.xml)
+            including read coverage, read assignments, and contiguous sequences
+            generated by combining the reads. The PathoDB is an optional module
+            that provides additional annotation (organism taxonomic lineage, gene
+            loci, protein products) for all sequences identified in the sample.
+            The PathoQC module can be used to preprocess the reads prior to
+            alignment with PathoMap.
+        </readme>
+    </package>
+</tool_dependency>