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2
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1 <tool id="p_chunks" name="PIMA: pChunks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>annotate plasmids</description>
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0
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import os
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9
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10 #set plasmid_db_name = $os.path.join($plasmid_database.extra_files_path, 'blastdb')
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11
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12 mkdir 'output_dir' &&
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13
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14 export BLASTDB='$plasmid_database.extra_files_path' &&
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15 Rscript '${__tool_directory__}/p_chunks.R'
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16 --plasmid_psl '$plasmid_psl'
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17 --plasmid_database '$plasmid_db_name'
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18 --no_amr
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19 --no_inc
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20 --output 'output_dir'
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21 --threads \${GALAXY_SLOTS:-4}
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22 && cat `readlink output_dir/plasmids.tsv` > '$output_plasmids'
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23 ]]></command>
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24 <inputs>
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25 <param argument="--plasmid_psl" type="data" format="psl" label="PSL file"/>
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26 <param argument="--plasmid_database" type="data" format="blastdbn" label="BLAST database of the plasmid sequences" help="Plasmid sequences are typically contianed in file named plasmids_and_vectors.fasta"/>
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27 </inputs>
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28 <outputs>
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29 <data name="output_plasmids" format="tsv" label="${tool.name} on ${on_string} (plasmids)"/>
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30 </outputs>
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31 <tests>
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32 <!-- Tests are not possible due to file size requirements -->
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33 </tests>
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34 <help>
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35 **What it does**
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36
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37 Accepts a PSL file and a BLAST database of the associated plasmid sequences and produces a tabular file containing query name,
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38 plasmid name, plasmid accession, query size, aligned bases, plasmid size and missing plasmids.
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39 </help>
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40 <expand macro="citations"/>
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41 </tool>
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42
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