annotate biom_normalize_table.xml @ 4:c96b40e55311 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit ddde8018cc6ff30dbb448e66be5433ce36e56b55

<tool id="biom_normalize_table" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <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 normalize-table
              --input-fp '$input_fp'
              --output-fp '$output_fp'
              $relative_abund
              $presence_absence
              --axis '$axis'
        ]]>
    </command>
    <inputs>
        <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
        <param name="relative_abund" argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
        <param name="presence_absence" argument="--presence-absence" type="boolean" checked="True" truevalue="--presence-absence" falsevalue="" label="Convert table to presence/absence" />
        <param argument="--axis" type="select" label="The axis to normalize over">
            <option value="sample" selected="True">Sample</option>
            <option value="observation">Observation</option>
        </param>
    </inputs>
    <outputs>
        <data format="biom1" name="output_fp"/>
    </outputs>
    <tests>
        <test>
            <param name="input_fp" value="input_abundance_1.biom1" />
            <param name="relative_abund" value="--relative-abund" />
            <param name="presence_absence" value="" />
            <param name="axis" value="sample" />
            <output name="output_fp" value="normalized_relative_abund_samples.biom" ftype="biom1" compare="sim_size"/>
        </test>
        <test>
            <param name="input_fp" value="input_abundance_1.biom1" />
            <param name="relative_abund" value="" />
            <param name="presence_absence" value="--presence-absence" />
            <param name="axis" value="observation" />
            <output name="output_fp" value="normalized_presence_absence_observations.biom" ftype="biom1" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
Normalize the values of a BIOM table through various methods. Relative abundance will take the relative abundance of each observation in terms of samples or observations.  Presence absensece will convert observations to 1's and 0's based on presence of the observation.
    ]]></help>
    <expand macro="citations" />
</tool>