<tool id="biom_subset_table" name="Subset" version="@VERSION@.1">
    <description>a BIOM table</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
        <![CDATA[
            biom subset-table
              --input-json-fp '$input_json_fp'
              --output-fp '$output_fp'
              --axis '$axis'
              --ids '$ids'
        ]]>
    </command>
    <inputs>
        <param name="input_json_fp" argument="--input-json-fp" type="data" format="biom1" label="BIOM table to subset" />
        <param argument="--axis" type="select" label="The axis to subset over">
            <option value="sample" selected="True">Sample</option>
            <option value="observation">Observation</option>
        </param>
        <param argument="--ids" type="data" format="text,tabular" label="file containing a single column of IDs to retain" />
    </inputs>
    <outputs>
        <data format="biom1" name="output_fp"/>
    </outputs>
    <tests>
        <test>
            <param name="input_json_fp" value="input_abundance_1.biom1" />
            <param name="axis" value="sample" />
            <param name="ids" value="sample_subsetting" />
            <output name="output_fp" file="subset_samples.biom" ftype="biom1" compare="sim_size"/>
        </test>
        <test>
            <param name="input_json_fp" value="input_abundance_1.biom1" />
            <param name="axis" value="observation" />
            <param name="ids" value="observation_subsetting" />
            <output name="output_fp" file="subset_observations.biom" ftype="biom1" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Subset a BIOM table, over either observations or samples, without fully parsing it. This command is intended to assist in working with very large tables when tight on memory, or as a lightweight way to subset a full table. Currently, it is possible to produce tables with rows or columns (observations or samples) that are fully zeroed.
    ]]></help>
    <expand macro="citations" />
</tool>