<tool profile="16.07" id="mothur_summary_tax" name="Summary.tax" 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@

        ## create symlinks to input datasets
        ln -s "$tax.taxonomy" tax.taxonomy.dat &&
        ln -s "$name" name.dat &&
        ln -s "$group" group.dat &&
        ln -s "$count" count.dat &&
        #if $reftax.source2:
            ln -s "$reftax.reftaxonomy" myreftax.taxonomy &&
            ln -s "$sum" myreftax.tree.sum &&
        #end if

        echo 'summary.tax(
            taxonomy=tax.taxonomy.dat,
            #if $name:
                name=name.dat,
            #end if
            #if $group:
                group=group.dat,
            #end if
            #if $reftax.source2:
                reftaxonomy=myreftax.taxonomy,
            #end if
            #if $count:
                count=count.dat,
            #end if
            relabund=$relabund
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="tax">
            <param name="source" type="select" label="Select Taxonomy from" help="">
                <option value="hist">History</option>
                <option value="ref">Cached Reference</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>
        <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/>
        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
        <conditional name="reftax">
            <param name="source2" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static.">
                <option value="" selected="true">Selection is Optional</option>
                <option value="hist">History</option>
                <option value="ref">Cached Reference</option>
            </param>
            <when value="ref">
                <param name="reftaxonomy" type="select" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified">
                    <options from_data_table="mothur_taxonomy"/>
                </param>
                <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
            </when>
            <when value="hist">
                <param name="reftaxonomy" type="data" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/>
                <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/>
            </when>
            <when value=""/>
        </conditional>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <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="taxsummary" format="mothur.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/>
    </outputs>
    <tests>
        <test>
            <param name="source" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="source" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="source2" value="hist"/>
            <param name="reftaxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="sum" value="abrecovery.pds.wang.tree.sum"/>
            <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information.

.. _summary.tax: https://www.mothur.org/wiki/Summary.tax
]]>
    </help>
    <expand macro="citations"/>
</tool>