<tool id="qiime_summarize_taxa" name="Summarize taxa" version="@WRAPPER_VERSION@.0">
    <description>and store results in a new table or appended to an existing mapping file (summarize_taxa)</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <version_command>summarize_taxa.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
summarize_taxa.py
    -i '$otu_table_fp'
    -o summarize_taxa
    -L '$level'
    #if str($mapping) != 'None':
        -m '$mapping'
    #end if
    --md_identifier $md_identifier
    $md_as_string
    $absolute_abundance
    #if str( $lower_percentage )
        -l $lower_percentage
    #end if
    #if str( $upper_percentage)
        -u $upper_percentage
    #end if
    $transposed_output
    $suppress_classic_table_output
    $suppress_biom_table_output
    ]]></command>
    <inputs>
        <param argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table"/>
        <param argument="--level" type="select" label="Taxonomic level to summarize by" multiple="true" display="checkboxes">
            <option value="1">Kingdom</option>
            <option value="2" selected="true">Phylum</option>
            <option value="3" selected="true">Class</option>
            <option value="4" selected="true">Order</option>
            <option value="5" selected="true">Family</option>
            <option value="6" selected="true">Genus</option>
            <option value="7">Species</option>
        </param>
        <param argument="--mapping" type="data" format="tabular,tsv,csv" label="Input metadata mapping" optional="true" help="If supplied, then the taxon information will be added to this file. This option is useful for coloring PCoA plots by taxon abundance or to perform statistical tests of taxon/mapping associations"/>
        <param argument="--md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key"/>
        <param argument="--md_as_string" type="boolean" truevalue="--md_as_string" falsevalue="" checked="false" label="Include metadata as string?" help="By default, metadata is included as list"/>
        <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Report absolute abundance?" help="By default, relative abundance is reported"/>
        <param argument="--lower_percentage" type="float" value="" optional="true" label="Percentage threshold to remove highly present OTU" help="If present, OTUs having higher absolute abundance are trimmed. To remove OTUs that make up more than 5% of the total dataset you would pass 0.05"/>
        <param argument="--upper_percentage" type="float" value="" optional="true" label="Percentage threshold to remove lowly present OTU" help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45"/>
        <param argument="--transposed_output" type="boolean" truevalue="--transposed_output" falsevalue="" checked="false" label="Transpose output?" help="If checked, the output will be written transposed from the regular output. This is helpful in cases when you want to use Site Painter to visualize your data"/>
        <param argument="--suppress_classic_table_output" type="boolean" truevalue="--suppress_classic_table_output" falsevalue="" checked="false" label="Suppress creation of the classic (TSV) format taxon table?" help="This option is ignored if a mapping file is present"/>
        <param argument="--suppress_biom_table_output" type="boolean" truevalue="--suppress_biom_table_output" falsevalue="" checked="false" label="Suppress creation of the BIOM-formatted taxon table?" help="This option is ignored if a mapping file is present"/>
    </inputs>
    <outputs>
        <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" label="${tool.name} on ${on_string}: L1 tab">
            <filter>"1" in level and suppress_classic_table_output is false</filter>
        </data>
        <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab">
            <filter>"2" in level and suppress_classic_table_output is false</filter>
        </data>
        <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab">
            <filter>"3" in level and suppress_classic_table_output is false</filter>
        </data>
        <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab">
            <filter>"4" in level and suppress_classic_table_output is false</filter>
        </data>
        <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab">
            <filter>"5" in level and suppress_classic_table_output is false</filter>
        </data>
        <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab">
            <filter>"6" in level and suppress_classic_table_output is false</filter>
        </data>
        <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" label="${tool.name} on ${on_string}: L7 tab">
            <filter>"7" in level and suppress_classic_table_output is false</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>
            <param name="level" value="2,3,4,5,6"/>
            <param name="mapping" value="summarize_taxa/map.txt"/>
            <param name="md_identifier" value="taxonomy"/>
            <param name="md_as_string" value=""/>
            <param name="absolute_abundance" value=""/>
            <param name="transposed_output" value=""/>
            <param name="suppress_classic_table_output" value=""/>
            <param name="suppress_biom_table_output" value=""/>
            <output name="L2_tab" value="summarize_taxa/1_L2.txt"/>
            <output name="L3_tab" value="summarize_taxa/1_L3.txt"/>
            <output name="L4_tab" value="summarize_taxa/1_L4.txt"/>
            <output name="L5_tab" value="summarize_taxa/1_L5.txt"/>
            <output name="L6_tab" value="summarize_taxa/1_L6.txt"/>
        </test>
        <test>
            <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>
            <param name="level" value="3,6"/>
            <param name="md_identifier" value="taxonomy"/>
            <param name="md_as_string" value=""/>
            <param name="absolute_abundance" value=""/>
            <param name="transposed_output" value=""/>
            <param name="suppress_classic_table_output" value=""/>
            <param name="suppress_biom_table_output" value=""/>
            <output name="L3_tab" value="summarize_taxa/2_L3.txt"/>
            <output name="L6_tab" value="summarize_taxa/2_L6.txt"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input.

More information about this tool is available on
`QIIME documentation <http://qiime.org/scripts/summarize_taxa.html>`_.
    ]]></help>
    <citations>
        <expand macro="citations"/>
    </citations>
</tool>