<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" optional="true" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
        <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" optional="true" 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>
        <expand macro="param-savelog"/>
    </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"/>
            <param name="savelog" value="true"/>
            <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"/>
            <param name="savelog" value="true"/>
            <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>