<tool id="biom_summarize_table" name="Summarize sample or observation data" version="@VERSION@.1">
    <description>in a BIOM table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
        <![CDATA[
            biom summarize-table
              --input-fp '$input_fp'
              --output-fp '$output_fp'
              $qualitative
              $observations
        ]]>
    </command>
    <inputs>
        <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table" />
        <param argument="--qualitative" type="boolean" checked="True" truevalue="--qualitative" falsevalue="" label="Present counts as number of unique observation ids per sample, rather than counts of observations per sample" />
        <param argument="--observations" type="boolean" checked="True" truevalue="--observations" falsevalue="" label="Summarize over observations" />
    </inputs>
    <outputs>
        <data format="text" name="output_fp"/>
    </outputs>
    <tests>
        <test>
            <param name="input_fp" value="input_abundance_1.biom1" />
            <param name="qualitative" value="" />
            <param name="observations" value="" />
            <output name="output_fp" value="summarize" compare="sim_size"/>
        </test>
        <test>
            <param name="input_fp" value="input_abundance_1.biom1" />
            <param name="qualitative" value="--qualitative" />
            <param name="observations" value="--observations" />
            <output name="output_fp" value="summarize_qualitative_observations" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Provides details on the observation counts per sample, including summary statistics, as well as metadata categories associated with samples and observations.
    ]]></help>
    <expand macro="citations" />
</tool>