<commit_before><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[
more $genome &&
run_FragGeneScan.pl
    -genome='$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_5 for 454 pyrosequencing reads with about 0.5% error rate</option>
            <option value="454_10">454_10 for 454 pyrosequencing reads with about 1% error rate</option>
            <option value="454_30">454_30 for 454 pyrosequencing reads with about 3% error rate</option>
            <option value="complete">complete for complete genomic sequences or short sequence reads without sequencing error</option>
            <option value="gene">gene</option>
            <option value="illumina_1">illumina_1 for Illumina sequencing reads with about 0.01% error rate</option>
            <option value="illumina_5">illumina_5 for Illumina sequencing reads with about 0.5% error rate</option>
            <option value="illumina_10">illumina_10 for Illumina sequencing reads with about 1% error rate</option>
            <option value="noncoding">noncoding</option>
            <option value="pwm">pwm</option>
            <option value="rgene">rgene</option>
            <option value="sanger_5">sanger_5 for Sanger sequencing reads with about 0.5% error rate</option>
            <option value="sanger_10">sanger_10 for Sanger sequencing reads with about 1% error rate</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. 

FragGeneScan was first released through omics website (http://omics.informatics.indiana.edu/FragGeneScan/ ) in March 2010, where you can find its old releases. FragGeneScan migrated to SourceForge in October, 2013. For users' convenience, we also make FragGeneScan available at GitHub: (https://github.com/COL-IU/FragGeneScan ).
    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkq747</citation>
    </citations>
</tool><commit_msg>cleanups<commit_after><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='$train'
    -thread=\${GALAXY_SLOTS:-4}
    ]]></command>
    <inputs>
        <param argument="-genome" type="data" format="fasta" label="Input equence file"/>
        <param argument="-complete" type="boolean" truevalue="1" falsevalue="0" label="Does the sequence file have complete genomic sequences?"/>
        <param argument="-train" type="select" label="Model">
            <option value="454_5">454_5 for 454 pyrosequencing reads with about 0.5% error rate</option>
            <option value="454_10">454_10 for 454 pyrosequencing reads with about 1% error rate</option>
            <option value="454_30">454_30 for 454 pyrosequencing reads with about 3% error rate</option>
            <option value="complete">complete for complete genomic sequences or short sequence reads without sequencing error</option>
            <option value="gene">gene</option>
            <option value="illumina_1">illumina_1 for Illumina sequencing reads with about 0.01% error rate</option>
            <option value="illumina_5">illumina_5 for Illumina sequencing reads with about 0.5% error rate</option>
            <option value="illumina_10">illumina_10 for Illumina sequencing reads with about 1% error rate</option>
            <option value="noncoding">noncoding</option>
            <option value="pwm">pwm</option>
            <option value="rgene">rgene</option>
            <option value="sanger_5">sanger_5 for Sanger sequencing reads with about 0.5% error rate</option>
            <option value="sanger_10">sanger_10 for Sanger sequencing reads with about 1% error rate</option>
            <option value="start">start</option>
            <option value="start1">start1</option>
            <option value="stop">stop</option>
            <option value="stop1">stop1</option>
        </param>
    </inputs>
    <outputs>
        <data name="coord" format="tabular" from_work_dir="output_file_name.out" label="${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>
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