<tool id="phyloseq_from_dada2" name="Create phyloseq object" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
  <description>from dada2 sequence and taxonomy tables</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
Rscript '${__tool_directory__}/phyloseq_from_dada2.R' 
--sequence_table '$sequence_table' 
--taxonomy_table '$taxonomy_table' 
#if $sample_table
    --sample_table '$sample_table' 
#end if
--output '$output'
    ]]></command>
    <inputs>
        <param name="sequence_table" type="data" format="dada2_sequencetable" label="Sequence table" help="Produced by the dada2 removeBimeraDenovo tool"/>
        <param name="taxonomy_table" type="data" format="tabular" label="Taxonomy table" help="Produced by the dada2 assignTaxonomyAndAddSpecies tool"/>
        <param name="sample_table" type="data" format="tabular" optional="true" label="Sample table" help="Rows are sample names, Columns are properties"/>
    </inputs>
    <outputs>
        <data name="output" format="phyloseq"/>
    </outputs>
    <tests>
        <test>
            <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
            <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
            <output name="output" ftype="phyloseq">
                <assert_contents>
                    <has_size value="4600" delta="400"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_text text="phyloseq-class experiment-level object"/>
                <has_text text="otu_table()   OTU Table:         [ 64 taxa and 2 samples ]"/>
                <has_text text="tax_table()   Taxonomy Table:    [ 64 taxa by 6 taxonomic ranks ]"/>
                <has_text text="refseq()      DNAStringSet:      [ 64 reference sequences ]"/>
                <has_n_lines n="4"/>
            </assert_stdout>
        </test>
        <test>
            <param name="sequence_table" value="sequence_table.dada2_sequencetable" ftype="dada2_sequencetable"/>
            <param name="taxonomy_table" value="taxonomy_table.tabular" ftype="tabular"/>
            <param name="sample_table" value="sample_data.tabular" ftype="tabular"/>
            <output name="output" ftype="phyloseq">
                <assert_contents>
                    <has_size value="4600" delta="400"/>
                </assert_contents>
            </output>
            <assert_stdout>
                <has_line line="phyloseq-class experiment-level object"/>
                <has_line line="otu_table()   OTU Table:         [ 64 taxa and 2 samples ]"/>
                <has_line line="sample_data() Sample Data:       [ 2 samples by 2 sample variables ]"/>
                <has_line line="tax_table()   Taxonomy Table:    [ 64 taxa by 6 taxonomic ranks ]"/>
                <has_line line="refseq()      DNAStringSet:      [ 64 reference sequences ]"/>
                <has_n_lines n="5"/>
            </assert_stdout>
        </test>
    </tests>
    <help>
**What it does**

Accepts a sequence table produced by the dada2 removeBimeraDenovo tool and a taxonomy table produced by the
dada2 assignTaxonomyAndAddSpecies tool and uses them to create a phyloseq object which is output in a phyloseq dataset.  
    </help>
    <expand macro="citations"/>
</tool>