<tool id="biom_from_uc" name="Create a BIOM table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>from a vsearch/uclust/usearch BIOM file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
        <![CDATA[
            biom from-uc
                --input-fp '$input_fp'
                --output-fp '$output_fp'
                #if $rep_set_fp
                    --rep-set-fp '$rep_set_fp'
                #end if
        ]]>
    </command>
    <inputs>
        <param argument="--input-fp" type="data" format="txt" label="UC File" />
        <param argument="--rep-set-fp" type="data" format="fasta" optional="true" label="Fasta file containing representative sequences with where sequences are labeled with OTU identifiers, and description fields contain original sequence identifiers" help="This output is created, for example, by vsearch with the --relabel_sha1 --relabel_keep options."/>
    </inputs>
    <outputs>
        <data format="biom1" name="output_fp"/>
    </outputs>
    <tests>
        <test>
            <param name="input_fp" value="uc_table.uc" />
            <output name="output_fp" file="biom_from_uc.biom" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Create a BIOM table from a vsearch/uclust/usearch BIOM file.
    ]]></help>
    <expand macro="citations" />
</tool>