<tool profile="16.07" id="mothur_classify_seqs" name="Classify.seqs" version="@WRAPPER_VERSION@.0">
    <description>Assign sequences to taxonomy</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
        @SHELL_OPTIONS@

        ## enable mothur to find blast
        loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&

        ## create symlinks to input datasets
        ln -s "$fasta" fasta.dat &&
        ln -s "$alignment.template" alignment.template.dat &&
        ln -s "$tax.taxonomy" tax.taxonomy.dat &&
        ln -s "$count" count.dat &&
        ln -s "$name" name.dat &&

        echo 'classify.seqs(
            fasta=fasta.dat,
            reference=alignment.template.dat,
            taxonomy=tax.taxonomy.dat,
            method=$classify.method,
            #if $classify.method == "wang":
                ksize=$classify.ksize,
                iters=$classify.iters,
                cutoff=$classify.cutoff,
                probs=$classify.probs,
            #elif $classify.method == "knn":
                numwanted=$classify.numwanted,
                search=$classify.search.algorithm,
                #if $classify.search.algorithm == "kmer":
                    ksize=$classify.search.ksize,
                #elif $classify.search.algorithm == "blast":
                    match=$classify.search.match,
                    mismatch=$classify.search.mismatch,
                    gapopen=$classify.search.gapopen,
                    gapextend=$classify.search.gapextend,
                #end if
            #end if
            #if $count:
                count=count.dat,
            #end if
            #if $name:
                name=name.dat,
            #end if
            relabund=$relabund,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | ./mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="fasta" type="data" format="fasta" label="fasta - Candiate 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" 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" label="reference - Reference to align with" help=""/>
            </when>
        </conditional>
        <conditional name="tax">
            <param name="source2" type="select" label="Select Taxonomy from" help="">
                <option value="ref">Cached Reference</option>
                <option value="hist">History</option>
            </param>
            <when value="ref">
                <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference">
                    <options from_data_table="mothur_taxonomy"/>
                </param>
            </when>
            <when value="hist">
                <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/>
            </when>
        </conditional>
        <conditional name="classify">
            <param name="method" type="select" label="method - Select a classification method" help="">
                <option value="wang" selected="true">Bayesian (default)</option>
                <option value="knn">K-Nearest Neighbor (knn)</option>
            </param>
            <when value="wang">
                <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
                <param name="iters" type="integer" value="100" min="1" label="iters - iterations to do when calculating the bootstrap confidence score"/>
                <param name="cutoff" type="integer" value="0" min="0" label="cutoff - specify a bootstrap confidence threshold for your taxonomy"/>
                <param name="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
            </when>
            <when value="knn">
                <param name="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/>
                <conditional name="search">
                    <param name="algorithm" type="select" label="algorithm - " help="">
                        <option value="kmer" selected="true">Kmer (default)</option>
                        <option value="blast">BLAST</option>
                        <option value="suffix">Suffix Tree</option>
                        <option value="distance">Distance</option>
                    </param>
                    <when value="kmer">
                        <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
                    </when>
                    <when value="blast">
                        <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
                        <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
                        <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
                        <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
                    </when>
                    <when value="suffix"/>
                    <when value="distance"/>
                </conditional>
            </when>
        </conditional>
        <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/>
        <param name="name" type="data" format="mothur.names" label="names file" optional="true"/>
        <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/>
        <data name="tax_summary" format="mothur.tax.summary" from_work_dir="fasta*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
        <data name="tree_sum" format="tabular" from_work_dir="tax.taxonomy*.tree.sum" label="${tool.name} on ${on_string}: tree.sum"/>
    </outputs>
    <tests>
        <test><!-- test with wang method -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="source" value="hist"/>
            <param name="template" value="abrecovery.fasta" ftype="fasta"/>
            <param name="source2" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <output name="tax_summary" md5="d6f02a20cdf415fb84e394d0dab2314f" ftype="mothur.tax.summary"/>
            <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
                <assert_contents>
                    <has_text text="Bacteria"/>
                    <has_text text="U68589"/>
                </assert_contents>
            </output>
            <output name="tree_sum" md5="a6ae5cc82edd181082dd23f348b621d9" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with knn method -->
            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
            <param name="source" value="hist"/>
            <param name="template" value="abrecovery.fasta" ftype="fasta"/>
            <param name="source2" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="method" value="knn"/>
            <output name="tax_summary" md5="4931072238dcf29344f4a1e3332f3415" ftype="mothur.tax.summary"/>
            <output name="taxonomy_out" md5="1080c7676c1a1f4f429c7d8df6a62f47" ftype="mothur.seq.taxonomy"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with knn method and blast algorithm -->
            <param name="fasta" value="abrecovery.fasta" ftype="fasta"/>
            <param name="source" value="hist"/>
            <param name="template" value="abrecovery.fasta" ftype="fasta"/>
            <param name="source2" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="method" value="knn"/>
            <param name="algorithm" value="blast"/>
            <output name="tax_summary" md5="4d6e1fa3be9abe5f57b0660fe5ae5887" ftype="mothur.tax.summary"/>
            <output name="taxonomy_out" md5="1296e2a2c8efd58f9c840760bed55042" ftype="mothur.seq.taxonomy"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The classify.seqs_ command assigns sequences to chosen taxonomy outline.

.. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs


v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
]]>
    </help>
    <expand macro="citations"/>
</tool>