<tool id="reago" name="Reago" version="0.1.0">
    <description> to assemble rRNA</description>

    <requirements>
        <requirement type="package" version="1.1">infernal</requirement>
        <requirement type="package" version="1.5.7">genometools</requirement>
        <requirement type="package" version="1.1">reago</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" />
    </stdio>

    <command>
<![CDATA[
        #set $r1_output=$os.path.splitext($os.path.basename(str($r1_file)))[0]
        #set $r2_output=$os.path.splitext($os.path.basename(str($r2_file)))[0]

        python $__tool_directory__/format_reago_input_files.py 
            --r1_input $r1_file
            --r2_input $r2_file
            --r1_output $r1_output
            --r2_output $r2_output

        ; 
        python \${REAGO_DIR}/filter_input.py 
            $r1_output
            $r2_output
            .
            \${REAGO_DIR}/cm/ ab 4

        ;
        python \${REAGO_DIR}/reago.py 
            filtered.fasta 
            .
            -l $read_length
            -o $overlap
            -t $tip_size 
            -b $path_finding_parameter
]]>
    </command>

    <inputs>
        <param name="r1_file" type="data" format="fasta" label="R1 input sequence 
            file" help=""/>
        <param name="r2_file" type="data" format="fasta" label="R2 input sequence 
            file" help=""/>
        <param name="read_length" type="integer" min="1" max="1000" value="101" 
            label="Read length" help=""/>
        <param name="overlap" type="float" min="0" max="1" value="0.8" 
            label="Overlap" help=""/>
        <param name="tip_size" type="integer" min="0" max="1000" value="30" 
            label="Tip size" help=""/>
        <param name="path_finding_parameter" type="integer" min="2" max="11" 
            value="10" label="Path finding parameter" help=""/>
    </inputs>

    <outputs>
        <data format="fasta" name="full_genes" 
            from_work_dir="full_genes.fasta"
            label="Full genes of ${on_string} (Framebot)" />
        <data format="fasta" name="fragments" 
            from_work_dir="fragments.fasta"
            label="Fragment genes of ${on_string} (Framebot)" />
    </outputs>

    <tests>
        <test>
            <param name="r1_file" value="reago_sample_1.fasta"/>
            <param name="r2_file" value="reago_sample_2.fasta"/>
            <param name="read_length" value="101" />
            <param name="overlap" value="0.8" />
            <param name="error_correction" value="0.05" />
            <param name="tip_size" value="30" />
            <param name="path_finding_parameter" value="10"/>

            <output name="full_genes" file="reago_full_genes.fasta"/>
            <output name="fragments" file="reago_fragments.fasta"/>
        </test>
    </tests>

    <help>
<![CDATA[

**What it does**

Reago is tool to assembly 16S ribosomal RNA recovery from metagenomic data.
More information on `Github repository <https://github.com/chengyuan/reago-1.1>`_.

-----

**Input**

Sequence files with r1 and r2 are required. 

-----

**Parameters**

The parameters are 

    - The overlap percentage
    - The threshold for error correction
    - The tip size
    - The parameter for path finding

-----

**Output**

Reago produces two output files:

    - A sequence file with full genes
    - A sequence file with fragment genes

    ]]>
    </help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btv231</citation>
    </citations>
</tool>