<tool id="fraggenescan" name="FragGeneScan" version="@WRAPPER_VERSION@.0">
    <description>for finding (fragmented) genes in short reads</description>
    <macros>
        <token name="@WRAPPER_VERSION@">1.30</token>
    </macros>
    <requirements>
        <requirement type="package" version="@WRAPPER_VERSION@">fraggenescan</requirement>
    </requirements>
    <version_command>@WRAPPER_VERSION@</version_command>
    <command detect_errors="aggressive"><![CDATA[
run_FragGeneScan.pl
    -genome='$genome'
    -out="output_file_name"
    -complete='$complete'
    -train='$train'
    -thread=\${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param argument="-genome" type="data" format="fasta" label="Input equence file"/>
        <param argument="-complete" type="boolean" truevalue="1" falsevalue="0" label="Does the sequence file have complete genomic sequences?"/>
        <param argument="-train" type="select" label="Model">
            <option value="454_5">454 pyrosequencing reads with about 0.5% error rate (454_5)</option>
            <option value="454_10">454 pyrosequencing reads with about 1% error rate (454_10)</option>
            <option value="454_30">454 pyrosequencing reads with about 3% error rate (454_30)</option>
            <option value="complete">complete genomic sequences or short sequence reads without sequencing error (complete)</option>
            <option value="gene">gene</option>
            <option value="illumina_1">Illumina sequencing reads with about 0.01% error rate (illumina_1)</option>
            <option value="illumina_5">Illumina sequencing reads with about 0.5% error rate (illumina_5)</option>
            <option value="illumina_10">Illumina sequencing reads with about 1% error rate (illumina_10)</option>
            <option value="noncoding">noncoding</option>
            <option value="pwm">pwm</option>
            <option value="rgene">rgene</option>
            <option value="sanger_5">Sanger sequencing reads with about 0.5% error rate (sanger_5)</option>
            <option value="sanger_10">Sanger sequencing reads with about 1% error rate (sanger_10)</option>
            <option value="start">start</option>
            <option value="start1">start1</option>
            <option value="stop">stop</option>
            <option value="stop1">stop1</option>
        </param>
    </inputs>
    <outputs>
        <data name="coord" format="tabular" from_work_dir="output_file_name.out" label="${tool.name} on ${on_string}: Coordinates of putative genes"/>
        <data name="nt_seq" format="fasta" from_work_dir="output_file_name.ffn" label="${tool.name} on ${on_string}: Nucleotide equences of putative genes"/>
        <data name="prot_seq" format="fasta" from_work_dir="output_file_name.faa" label="${tool.name} on ${on_string}: Protein equences of putative genes"/>
        <data name="gff" format="gff" from_work_dir="output_file_name.gff" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="genome" value="contigs.fasta"/>
            <param name="complete" value="False"/>
            <param name="train" value="complete"/>
            <output name="coord" ftype="tabular" value="contigs.out"/>
            <output name="nt_seq" ftype="fasta" value="contigs.ffn"/>
            <output name="prot_seq" ftype="fasta" value="contigs.faa"/>
            <output name="gff" ftype="gff" value="contigs.gff"/>
        </test>
        <test>
            <param name="genome" value="NC_000913.fasta"/>
            <param name="complete" value="True"/>
            <param name="train" value="complete"/>
            <output name="coord" ftype="tabular" value="NC_000913.out"/>
            <output name="nt_seq" ftype="fasta" value="NC_000913.ffn"/>
            <output name="prot_seq" ftype="fasta" value="NC_000913.faa"/>
            <output name="gff" ftype="gff" value="NC_000913.gff"/>
        </test>
        <test>
            <param name="genome" value="NC_000913-454.fasta"/>
            <param name="complete" value="False"/>
            <param name="train" value="454_10"/>
            <output name="coord" ftype="tabular" value="NC_000913-454.out"/>
            <output name="nt_seq" ftype="fasta" value="NC_000913-454.ffn"/>
            <output name="prot_seq" ftype="fasta" value="NC_000913-454.faa"/>
            <output name="gff" ftype="gff" value="NC_000913-454.gff"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

FragGeneScan is an application for finding (fragmented) genes in short reads.
It can also be applied to predict prokaryotic genes in incomplete assemblies or complete genomes. 

    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkq747</citation>
    </citations>
</tool>