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<tool id="p_chunks" name="PIMA: pChunks" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
  <description>annotate plasmids</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os

#set plasmid_db_name = $os.path.join($plasmid_database.extra_files_path, 'blastdb')

mkdir 'output_dir' &&

export BLASTDB='$plasmid_database.extra_files_path' &&
Rscript '${__tool_directory__}/p_chunks.R' 
--plasmid_psl '$plasmid_psl'
--plasmid_database '$plasmid_db_name'
--no_amr
--no_inc
--output 'output_dir'
--threads \${GALAXY_SLOTS:-4}
&& cat `readlink output_dir/plasmids.tsv` > '$output_plasmids'
    ]]></command>
    <inputs>
        <param argument="--plasmid_psl" type="data" format="psl" label="PSL file"/>
        <param argument="--plasmid_database" type="data" format="blastdbn" label="BLAST database of the plasmid sequences" help="Plasmid sequences are typically contianed in file named plasmids_and_vectors.fasta"/>
    </inputs>
    <outputs>
        <data name="output_plasmids" format="tsv" label="${tool.name} on ${on_string} (plasmids)"/>
    </outputs>
    <tests>
        <test>
            <param name="plasmid_psl" value="input.psl" ftype="psl"/>
            <param name="plasmid_database" value="input.blastdbn" ftype="blastdbn"/>
            <output name="output_plasmids" value="output.tsv" ftype="tsv"/>
        </test>
    </tests>
    <help>
**What it does**

Accepts a PSL file and a BLAST database of the associated plasmid sequences and produces a tabular file containing query name,
plasmid name, plasmid accession, query size, aligned bases, plasmid size and missing plasmids.
    </help>
    <expand macro="citations"/>
</tool>