<tool profile="16.07" id="mothur_primer_design" name="Primer.design" version="@WRAPPER_VERSION@.0">
    <description>identify sequence fragments that are specific to particular OTUs</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 "$fasta" fasta.dat &&
        ln -s "$otu" otu.dat &&
        ln -s "$name" name.dat &&
        ln -s "$count" count.dat &&

        echo 'primer.design(
            fasta=fasta.dat,
            list=otu.dat,
            #if $label:
                label=$label,
            #end if
                otulabel=$otulabel,
            #if $name:
                name=name.dat,
            #end if
            #if $count:
                count=count.dat,
            #end if
            #if $cutoff:
                cutoff=$cutoff,
            #end if
            #if $mintm:
                mintm=$mintm,
            #end if
            #if $maxtm:
                maxtm=$maxtm,
            #end if
            pdiffs=$pdiffs,
            length=$length,
            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" label="fasta - provide aligned fasta file"/>
        <param name="otu" type="data" format="mothur.list" label="list - OTU list file"/>
        <param name="label" type="select" optional="true" multiple="false" label="label - OTU Labels" help="If none selected, the first label in your file will be used">
            <expand macro="labeloptions"/>
        </param>
        <param name="otulabel" type="select" optional="false" multiple="false" label="otulabel - choose an OTU name">
            <options>
                <filter type="data_meta" ref="otu" key="otulabels"/>
            </options>
        </param>
        <param name="name" type="data" format="mothur.names" optional="true" label="name - names file associated with your fasta file"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count table associated with your fasta file"/>
        <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - specify the number of differences allowed in the primer" help=""/>
        <param name="length" type="integer" value="18" min="0" label="length - indicate the length of the primer" help=""/>
        <param name="mintm" type="integer" value="" optional="true" label="mintm - indicate minimum melting temperature" help=""/>
        <param name="maxtm" type="integer" value="" optional="true" label="maxtm - indicate maximum melting temperature" help=""/>
        <param name="cutoff" type="integer" value="" optional="true" min="0" max="100" label="cutoff - set a percentage of sequences that support the base" help="For example: cutoff=97 would only return a sequence that only showed ambiguities for bases that were not supported by at least 97% of sequences."/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="fasta_out" format="mothur.align" from_work_dir="otu*.cons.fasta" label="${tool.name} on ${on_string}: cons.fasta"/>
        <data name="summary_out" format="tabular" from_work_dir="otu*.primer.summary" label="${tool.name} on ${on_string}: primer.summary"/>
        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
    </outputs>
    <tests>
        <test>
            <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
            <param name="otu" value="amazon.align_head.list" ftype="mothur.list"/>
            <param name="otulabel" value="Otu1"/>
            <param name="label" value="0.30"/>
            <output name="fasta_out" md5="a5c8c17814f02124194dba2e37f566c7" ftype="mothur.align"/>
            <output name="summary_out" md5="8dd341c49c26c6d0f8026b34cb7bc925" ftype="tabular"/>
            <output name="list_out" md5="0a73804f3d48c668b4dab85c76d2c767" ftype="mothur.list"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The primer.design_ allows you to identify sequence fragments that are specific to particular OTUs.

.. _primer.design: https://www.mothur.org/wiki/Primer.design

]]>
    </help>
    <citations>
        <citation type="doi">10.1128/AEM.01541-09</citation>
    </citations>
</tool>