annotate reago.xml @ 0:13dd84cab09e draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/reago commit f5be73e67192909db96dfab214f4360eb41757a4

<tool id="reago" name="Reago" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
    <description> to assemble rRNA</description>
    <macros>
        <token name="@TOOL_VERSION@">1.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">reago</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">reago</requirement>
        <requirement type="package" version="1.11">networkx</requirement>
    </requirements>
    <command detect_errors="exit_code">
    <![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'

        &&  
        filter_input.py 
            '$r1_output'
            '$r2_output'
            .
            \$(dirname \$(which reago.py))/cm/ 
            $cm_to_use
            "\${GALAXY_SLOTS:-4}"

        && 
        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="(-l)"/>

        <param name="overlap" type="float" min="0" max="1" value="0.8" 
            label="Overlap" help="(-o)"/>

        <param name="tip_size" type="integer" min="0" max="1000" value="30" 
            label="Tip size" help="(-t)"/>

        <param name="path_finding_parameter" type="integer" min="2" max="11" 
            value="10" label="Path finding parameter" help="(-b)"/>

        <param name="cm_to_use" type="select" label="Database to use to to identify 16S reads" help="">
            <option value="b">Bacteria only</option>
            <option value="a">Archea only</option>
            <option value="ab">Bacteria and archea</option>
        </param>
    </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="tip_size" value="30" />
            <param name="path_finding_parameter" value="10"/>
            <param name="cm_to_use" value="ab" />
            <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>