<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 &&

echo 'summary.tax(
    taxonomy=tax.taxonomy.dat,
    #if $name:
        name=name.dat,
    #end if
    #if $group:
        group=group.dat,
    #end if
    #if $count:
        count=count.dat,
    #end if
    relabund=$relabund,
    threshold=$threshold,
    output=$output,
    printlevel=$printlevel
)'
| 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"/>
        <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"/>
        <param name="threshold" type="integer" value="0" min="0" label="threshold- specify a cutoff for the taxonomy file"
            help="Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the concensus.
            This feature is similar to adjusting the cutoff in classify.seqs"/>
        <expand macro="param-output"/>
        <expand macro="param-printlevel"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="taxsummary" format="mothur.tax.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" ftype="mothur.tax.summary">
                <assert_contents>
                    <expand macro="test-taxsummary-format"/>
                    <has_text text="Root"/>
                    <has_text text="Bifidobacterium"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="source" value="hist"/>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <output name="taxsummary" ftype="mothur.tax.summary">
                <assert_contents>
                    <expand macro="test-taxsummary-format"/>
                    <has_text text="Root"/>
                    <has_text text="Bifidobacterium"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <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>