view biom_normalize_table.xml @ 10:60a9ca72b006 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 950bc3657a7bd6975337324bd0f1d0e5c0afc0f4

<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="bio_tools"/>
    <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>