<?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>