annotate biom_normalize_table.xml @ 7:e34a4fe24d77 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4d77c1e4bd9f6876ee338858a8cd4c7e9528d54c

<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 argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
        <param argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
        <param 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>