<tool id="humann2_rna_dna_norm" name="Normalize" version="@WRAPPER_VERSION@.0">
    <description> combined meta'omic sequencing data</description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann2_rna_dna_norm
    --input_dna '$input_dna'
    --input_rna '$input_rna'
    --output_basename 'results'
    --method '$method'
    #if $log.log_transform == 'yes'
        --log_transform
        --log_base $log.log_base
    #end if
    ]]></command>
    <inputs>
        <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
        <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
        <param argument="--method" type="select" label="Choice of smoothing method">
            <option value="laplace">Laplace</option>
            <option value="witten_bell">Witten-Bell</option>
        </param>
        <conditional name="log">
            <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
                <option value="yes">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
            </when>
            <when value="no"/>
        </conditional>
    </inputs>
    <outputs>
        <data format="tsv" name="results-relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: normalized RNA"/>
        <data format="tsv" name="results-smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: smoothed DNA"/>
        <data format="tsv" name="results-smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: smoothed RNA"/>
    </outputs>
    <tests>
        <test>
            <param name="input_dna" value="rna_dna_norm-dna.txt"/>
            <param name="input_rna" value="rna_dna_norm-rna.txt"/>
            <param name="method" value="laplace"/>
            <conditional name="log">
                <param name="log_transform" value="no"/>
            </conditional>
            <output name="results-relative_expression" md5="193000abf357cb14f70273ba6cd5f095"/>
            <output name="results-smoothed_dna" md5="3767aa13988a4dca40a07cb6970bcc60"/>
            <output name="results-smoothed_rna" md5="8b1bcb819c31ef0ba5ab4975582bfcf7"/>
        </test>
        <test>
            <param name="input_dna" value="rna_dna_norm-dna.txt"/>
            <param name="input_rna" value="rna_dna_norm-rna.txt"/>
            <param name="method" value="witten_bell"/>
            <conditional name="log">
                <param name="log_transform" value="yes"/>
                <param name="log_base" value="2"/>
            </conditional>
            <output name="results-relative_expression" md5="3064e6377c074c6e6e9cf7fdfd466ec9"/>
            <output name="results-smoothed_dna" md5="3a1203c0986d79e9cb4ac0e3a4a89f4e"/>
            <output name="results-smoothed_rna" md5="1038b44e52b95a867dc6341b4dd91697"/>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Given a DNA table and a RNA table, produce smoothed RNA and DNA values as well as relative expression values. "Smoothing" means substituting a small value in place of a zero or missing value. The default method used is "Laplace" (pseudocount) scaling, where the pseudocount is the sample-specific minimum non-zero value. (Witten-Bell smoothing is also implemented.)
    ]]></help>
    <expand macro="citations"/>
</tool>