<tool profile="16.07" id="mothur_create_database" name="Create.database" version="@WRAPPER_VERSION@.0">
    <description>creates a database file from a list, repnames, repfasta and contaxonomy file</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 "$otu" otu.dat &&
        ln -s "$repfasta" repfasta.dat &&
        ln -s "$nameOrCount" nameOrCount.dat &&
        ln -s "$constaxonomy" constaxonomy.dat &&
        ln -s "$group" group.dat &&

        echo 'create.database(
            #if $otu.is_of_type("mothur.list"):
                list=otu.dat
            #elif $otu.is_of_type("mothur.shared"):
                shared=otu.dat
            #end if
            ,repfasta=repfasta.dat
            #if $nameOrCount.is_of_type("mothur.names"):
                ,repname=nameOrCount.dat
            #elif $nameOrCount.is_of_type("mothur.count_table"):
                ,count=nameOrCount.dat
            #end if
            ,constaxonomy=constaxonomy.dat
            #if $group:
                ,group=group.dat
            #end if
            #if $label:
                ,label=$label
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/>
        <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
        <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="repname/count - Representative sequences" help="rep.name file or rep.count_table file generated by get.oturep"/>
        <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/>
        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
        <param name="label" type="select" label="label - OTU Labels" optional="true" help="Select exactly one label. If none selected, first label in your list or shared file will be used">
            <expand macro="labeloptions"/>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/>
    </outputs>
    <tests>
        <!-- Test with a mothur.names file -->
        <test>
            <param name="otu" value="cd-test.list" ftype="mothur.list"/>
            <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
            <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/>
            <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
            <param name="label" value="unique"/>
            <output name="database" file="cd-test.database" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <!-- Test with a mothur.count_table file -->
        <test>
            <param name="otu" value="cd-test.list" ftype="mothur.list"/>
            <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
            <param name="nameOrCount" value="cd-test.count_table" ftype="mothur.count_table"/>
            <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
            <param name="label" value="unique"/>
            <output name="database" file="cd-test.database" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file.

.. _list: https://www.mothur.org/wiki/List_file
.. _shared: https://www.mothur.org/wiki/Shared_file
.. _create.database: https://www.mothur.org/wiki/Create.database

v.1.28.0: Updated to Mothur 1.33, added count paramter.

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