<tool id="humann_rna_dna_norm" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description> combined meta'omic sequencing data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
humann_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 $log.log_base
#end if
    ]]></command>
    <inputs>
        <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
        <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
        <param argument="--method" type="select" label="Choice of smoothing method">
            <option value="laplace">Laplace</option>
            <option value="witten_bell">Witten-Bell</option>
        </param>
        <conditional name="log">
            <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
                <option value="yes">Yes</option>
                <option value="no">No</option>
            </param>
            <when value="yes">
                <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
            </when>
            <when value="no"/>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: Normalized RNA"/>
        <data format="tabular" name="smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: Smoothed DNA"/>
        <data format="tabular" name="smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: Smoothed RNA"/>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <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="relative_expression" ftype="tabular">
                <assert_contents>
                    <has_text text="A|1"/>
                    <has_text text="0.285714"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output name="smoothed_dna" ftype="tabular">
                <assert_contents>
                    <has_text text="A|1"/>
                    <has_text text="13"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output name="smoothed_rna" ftype="tabular">
                <assert_contents>
                    <has_text text="A|1"/>
                    <has_text text="62"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="3">
            <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="relative_expression" ftype="tabular">
                <assert_contents>
                    <has_text text="A|1"/>
                    <has_text text="0.118644"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output name="smoothed_dna" ftype="tabular">
                <assert_contents>
                    <has_text text="A|1"/>
                    <has_text text="9.24"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
            <output name="smoothed_rna" ftype="tabular">
                <assert_contents>
                    <has_text text="A|1"/>
                    <has_text text="39.4545"/>
                    <has_n_columns n="3"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Given a DNA table and a RNA table, this tool produces 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.)

The DNA and RNA columns must be 1:1 and in the same order.

If working with stratified data, smoothing is carried out on the stratified values and then community totals are recomputed.
    ]]></help>
    <expand macro="citations"/>
</tool>