<tool id="isescan" name="ISEScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description> Insertion Sequence Elements detection in prokaryotic genomes </description>
    <macros>
        <import>macro.xml</import>
    </macros>
    <expand macro='xrefs'/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
        isescan.py
        --seqfile '$input_file'
        --output 'results'
        $remove_short_is
        --nthread \${GALAXY_SLOTS:-7}
        | tee '$logfile'

    ]]>
    </command>
    <inputs>
        <param name="input_file" type="data" format="fasta,fasta.gz" label="Genome fasta input" help="Fasta sequence to analyse for IS"/>
        <param name="remove_short_is" argument="--removeShortIS" type="boolean" truevalue="--removeShortIS" falsevalue=""
               label="Remove incomplete IS elements"
               help="Remove partial IS elements which include IS element with length &gt; 400 or single copy IS element without perfect TIR"/>
        <param name="output_format" type="select" label="Output format type" help="Choose an output file format">
            <option value="raw"> Raw format (txt) </option>
            <option value="csv"> Coma separate file (CSV) </option>
            <option value="tsv" selected="true"> Tabular separate file (TSV) </option>
        </param>
        <param name="log_activate" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Keep the log file"/>
    </inputs>
    <outputs>
        <data name="summary" format="txt" label="${tool.name} on ${on_string}: Summary of detected IS"/>
        <data name="is_results" format="tabular" label="${tool.name} on ${on_string}: IS detected">
          <change_format>
              <when input="output_format" value="raw" format="txt"/>
              <when input="output_format" value="csv" format="csv"/>
              <when input="output_format" value="tsv" format="tabular"/>
          </change_format>
        </data>
        <data name="gff_file" format="gff3" label="IS annotation"/>
        <data name="is_fasta" format="fasta" label="${tool.name} on ${on_string}: IS nucleic sequence"/>
        <data name="tpase_fasta" format="fasta" label="${tool.name} on ${on_string}: Transposase nucleic acid sequence"/>
        <data name="tpase_amino" format="fasta" label="${tool.name} on ${on_string}: Transposase amino acid sequence"/>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log file">
            <filter> log_activate == True </filter>
        </data>
    </outputs>
    <tests>
        <test> <!-- TEST_1 default parameters -->
            <param name="input_file" value="NC_012624.fna" />
            <output name="summary" value="TEST_1/test_1.fna.sum"/>
            <output name="is_results" value="TEST_1/test_1.fna.tsv"/>
            <output name="gff_file" value="TEST_1/test_1.fna.gff"/>
            <output name="is_fasta" value="TEST_1/test_1.fna.is.fna"/>
            <output name="tpase_fasta" value="TEST_1/test_1.fna.orf.fna"/>
            <output name="tpase_amino" value="TEST_1/test_1.fna.orf.faa"/>
            <output name="logfile" value="TEST_1/test_1.log" lines_diff="50"/>
        </test>
        <test> <!-- TEST_2 with remove_short_is and raw output-->
            <param name="input_file" value="NC_012624.fna"/>
            <param name="remove_short_is" value="true"/>
            <param name="output_format" value="raw"/>
            <output name="summary" value="TEST_2/test_2.fna.sum"/>
            <output name="is_results" value="TEST_2/test_2.fna.raw"/>
            <output name="gff_file" value="TEST_2/test_2.fna.gff"/>
            <output name="is_fasta" value="TEST_2/test_2.fna.is.fna"/>
            <output name="tpase_fasta" value="TEST_2/test_2.fna.orf.fna"/>
            <output name="tpase_amino" value="TEST_2/test_2.fna.orf.faa"/>
            <output name="logfile" value="TEST_2/test_2.log" lines_diff="50"/>
        </test>
        <test> <!-- TEST_3 without logfile and with csv output-->
            <param name="input_file" value="NC_012624.fna"/>
            <param name="remove_short_is" value="false"/>
            <param name="output_format" value="csv"/>
            <param name="log_activate" value="False"/>
            <output name="summary" value="TEST_3/test_3.fna.sum"/>
            <output name="is_results" value="TEST_3/test_3.fna.tsv"/>
            <output name="gff_file" value="TEST_3/test_3.fna.gff"/>
            <output name="is_fasta" value="TEST_3/test_3.fna.is.fna"/>
            <output name="tpase_fasta" value="TEST_3/test_3.fna.orf.fna"/>
            <output name="tpase_amino" value="TEST_3/test_3.fna.orf.faa"/>
        </test>
    </tests>
    <help><![CDATA[
        **What it does**
        With
        ]]>
    </help>
    <expand macro="citations"/>
</tool>