annotate biom_normalize_table.xml @ 6:516e071e9c66 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 5fc41e15cb372b3ae635c550c387ccd41af166f7

<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>