<tool profile="16.07" id="mothur_chimera_check" name="Chimera.check" version="@WRAPPER_VERSION@.0">
    <description>Find putative chimeras using chimeraCheck</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @SHELL_OPTIONS@

        ## create symlinks to input datasets
        ln -s "$fasta" fasta.dat &&
        ln -s "$alignment.template" alignment.template.dat &&
        #if $svg.gen == "yes":
            ln -s "$svg.name" svg.name.dat &&
        #end if

        echo 'chimera.check(
            fasta=fasta.dat,
            reference=alignment.template.dat,
            #if $svg.gen == "yes":
                svg=yes,
                name=svg.name.dat,
            #end if
            increment=$increment,
            ksize=$ksize,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/>
        <conditional name="alignment">
            <param name="source" type="select" label="Select Reference Template from" help="">
                <option value="hist">History</option>
                <option value="ref">Cached Reference</option>
            </param>
            <when value="ref">
                <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help="">
                    <options from_data_table="mothur_aligndb">
                    </options>
                </param>
            </when>
            <when value="hist">
                <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/>
            </when>
        </conditional>
        <param name="ksize" type="integer" value="7" argument="ksize" label="ksize - kmer length to determine differences between sequence fragments (uses default if &lt; 1)"/>
        <param name="increment" type="integer" value="10" argument="increment" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/>
        <conditional name="svg">
            <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help="">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param name="name" type="data" format="mothur.names" optional="true" argument="name" label="name - Names of queries for which to generate SVG plot"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="out_file" format="txt" from_work_dir="fasta.chimeracheck.chimeras" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/>
        <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images">
            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.chimeracheck\.svg"/>
            <filter>svg['gen'] == 'yes'</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <param name="source" value="hist"/>
            <param name="template" value="HMP_MOCK.v35.align"/>
            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
            <param name="source" value="hist"/>
            <param name="template" value="HMP_MOCK.v35.align"/>
            <param name="gen" value="yes"/>
            <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/>
            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
            <output_collection name="images" count="2">
                <element name="M00967_43_000000000-A3JHG_1_1101_14010_4122" file="M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg"/>
                <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows.

Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.

.. _chimera.check: https://www.mothur.org/wiki/Chimera.check

]]>
    </help>
    <expand macro="citations"/>
</tool>