<tool id="sigihmm" name="SigiHMM" version="3.8.0" profile="16.04">
    <description>Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models</description>
    <edam_topics>
        <edam_topic>topic_0194</edam_topic>
        <edam_topic>topic_0091</edam_topic>
    </edam_topics>
    <edam_operations>
        <edam_operation>operation_0362</edam_operation>
    </edam_operations>
    <requirements>
        <requirement type="package" version="3.8">colombo</requirement>
    </requirements>
    <version_command><![CDATA[ echo "3.8" ]]></version_command>
    <command detect_errors="exit_code"><![CDATA[
        #import os 
        #set input_l=$os.path.basename(str($input))+".embl" 
        #set output_l=$os.path.basename(str($output))+".embl" 
        ln -sf "$input" "$input_l" &&
        ln -sf "$output" "$output_l" &&
        #if $cut
            #set cut_l=$os.path.basename(str($cut))+".cut"
            ln -sf "$cut" "$cut_l" &&
        #end if
        #set gff_l=$os.path.basename(str($gff))+".gff"
        ln -sf "$gff" "$gff_l" &&
        
        SigiHMM input="`pwd`/$input_l" output="`pwd`/$output_l" sens=$sens outlier=$outlier phx=$phx join=$join gff="`pwd`/$gff_l"
        #if $cut
            cut="`pwd`/$cut_l"
        #end if
    ]]></command>
    <inputs>
        <param type="data" format="embl" name="input" argument="input" label="Input" optional="false" />
        <param type="data" format="cut" name="cut" argument="cut" label="Donor candidates CUT file" optional="true" />
        <param type="float" name="sens" argument="sens" label="PUTAL Sensitivity" optional="false" min="0" max="1.0" value="0.7" />
        <param type="boolean" name="outlier" argument="outlier" label="Assess Outliers" optional="false" truevalue="Yes" falsevalue="No" checked="false" />
        <param type="boolean" name="phx" argument="phx" label="Assess PHX" optional="false" truevalue="Yes" falsevalue="No" checked="true" />
        <param type="select" name="join" argument="join" label="Merge Islands Of Distance" optional="false" >
            <option value="0">0</option>
            <option value="1" selected="true">1</option>
            <option value="2">2</option>
            <option value="3">3</option>
        </param>
    </inputs>
    <outputs>
        <data format="embl" name="output" metadata_source="input" />
        <data format="gff" name="gff" label="${tool.name} on ${on_string} features" />
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- SigiHMM uses biojava which currently has a bug: https://github.com/biojava/biojava/issues/843 -->
            <param name="input" value="test-data/test.embl" ftype="embl" />
            <param name="join" value="3" />
            <output name="output" checksum="sha256:f87830fad329a0c47f734cffa069593be0423a064878bd894df8b8dc4b451c3d" ftype="embl" />
            <output name="gff" checksum="sha256:6af8fb320804803f54870c3e7b024d5e1305cee7e464e89355fba1f00f94ce44" ftype="gff" />
        </test>
        <test expect_failure="true">
            <!-- SigiHMM 3.8 crashes for an unknown reason on some datasets. v4.0 does not seem to have this issue. -->
            <param name="input" value="test-data/crash.embl" ftype="embl" />
            <param name="join" value="3" />
        </test>
    </tests>
    <help><![CDATA[
        https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-7-142
    ]]></help>
    <citations>
        <citation type="doi">10.5281/zenodo.3364789</citation>
        <citation type="doi">10.1186/1471-2105-7-142</citation>
    </citations>
</tool>