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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="perl" version="5.18.1">
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4 <repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="bowtie" version="0.12.7">
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7 <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="mirdeep2_mapper" version="2.0">
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10 <install version="1.0">
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11 <actions>
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12 <action type="download_by_url">https://raw.githubusercontent.com/bgruening/download_store/master/miRDeep2/miRDeep2-mapper.tar.gz</action>
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13 <action type="move_file">
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14 <source>clip_adapters.pl</source>
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15 <destination>$INSTALL_DIR</destination>
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16 </action>
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17 <action type="move_file">
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18 <source>collapse_reads_md.pl</source>
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19 <destination>$INSTALL_DIR</destination>
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20 </action>
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21 <action type="move_file">
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22 <source>convert_bowtie_output.pl</source>
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23 <destination>$INSTALL_DIR</destination>
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24 </action>
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25 <action type="move_file">
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26 <source>fastaparse.pl</source>
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27 <destination>$INSTALL_DIR</destination>
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28 </action>
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29 <action type="move_file">
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30 <source>fastq2fasta.pl</source>
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31 <destination>$INSTALL_DIR</destination>
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32 </action>
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33 <action type="move_file">
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34 <source>illumina_to_fasta.pl</source>
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35 <destination>$INSTALL_DIR</destination>
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36 </action>
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37 <action type="move_file">
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38 <source>mapper.pl</source>
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39 <destination>$INSTALL_DIR</destination>
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40 </action>
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41 <action type="move_file">
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42 <source>parse_mappings.pl</source>
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43 <destination>$INSTALL_DIR</destination>
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44 </action>
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45 <action type="move_file">
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46 <source>rna2dna.pl</source>
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47 <destination>$INSTALL_DIR</destination>
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48 </action>
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49 <action type="set_environment">
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50 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable>
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51 </action>
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52 </actions>
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53 </install>
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54 <readme>
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55
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56 Processes reads and/or maps them to the reference genome.
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57
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58 input:
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59 Default input is a file in fasta, seq.txt or qseq.txt format. More input can be given depending on the options used.
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60 output:
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61 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.
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62
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63 </readme>
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64 </package>
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65 </tool_dependency>
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