<?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>