<tool id="qiime_make_otu_heatmap" name="make otu heatmap" version="1.9.1galaxy1">
    <description>Plot heatmap of OTU table</description>
    
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <command>
<![CDATA[
        make_otu_heatmap.py 
            -i $otu_table_fp 
            -o make_otu_heatmap_output

            #if str($otu_tree) != 'None':
             -t $otu_tree
            #end if

            #if str($map_fname) != 'None':
             -m $map_fname
            #end if

            #if str($category):
             -c $category
            #end if

            #if str($sample_tree) != 'None':
             -s $sample_tree
            #end if

            #if $no_log_transform:
             --no_log_transform
            #end if

            #if $suppress_row_clustering:
             --suppress_row_clustering
            #end if

            #if $suppress_column_clustering:
             --suppress_column_clustering
            #end if

            #if $absolute_abundance:
             --absolute_abundance
            #end if

            #if str($ad.select) == "yes":
                #if $ad.color_scheme:
                    --color_scheme $ad.color_scheme
                #end if

                #if $ad.width:
                    --width $ad.width
                #end if

                #if $ad.height:
                    --height $ad.height
                #end if

                #if $ad.dpi:
                    --dpi $ad.dpi
                #end if

                #if $ad.obs_md_category:
                    --obs_md_category $ad.obs_md_category
                #end if

                #if $ad.obs_md_level:
                    --obs_md_level $ad.obs_md_level
                #end if
            #end if
]]>

    </command>

    <inputs>
        <param label="-i/--otu_table_fp: path to the input OTU table (i.e., the 
            output from make_otu_table.py)" name="otu_table_fp" optional="False" 
            type="data"/>
        <param default="None" label="-t/--otu_tree: Tree file to be used for 
            sorting OTUs in the heatmap" name="otu_tree" optional="True" 
            type="data"/>
        <param default="None" label="-m/--map_fname: Metadata mapping file to be 
            used for sorting Samples in the heatmap." name="map_fname" optional="True" 
            type="data"/>
        <param default="None" label="-c/--category: Metadata category for sorting 
            samples. Samples will be clustered within each category level using 
            euclidean UPGMA." name="category" optional="True" type="text"/>
        <param default="None" label="-s/--sample_tree: Tree file to be used for 
            sorting samples (e.g, output from upgma_cluster.py). If both this and 
            the sample mapping file are provided, the mapping file is ignored." 
            name="sample_tree" optional="True" type="data"/>
        <param label="--no_log_transform: Data will not be log-transformed. Without 
            this option, all zeros will be set to a small value (default is 1/2 
            the smallest non-zero entry). Data will be translated to be non-negative 
            after log transform, and num_otu_hits will be set to 0." 
            name="no_log_transform" selected="False" type="boolean"/>
        <param label="--suppress_row_clustering: No UPGMA clustering of OTUs (rows) 
            is performed. If --otu_tree is provided, this flag is ignored." 
            name="suppress_row_clustering" selected="False" type="boolean"/>
        <param label="--suppress_column_clustering: No UPGMA clustering of Samples 
            (columns) is performed. If --map_fname is provided, this flag is ignored." 
            name="suppress_column_clustering" selected="False" type="boolean"/>
        <param label="--absolute_abundance: Do not normalize samples to sum to 1.
            [default False]" name="absolute_abundance" selected="False" 
            type="boolean"/>

        <conditional name="ad">
            <param name="select" type="select" label="Show advanced options">
                <option value="no" selected="True">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">
                <param default="YlGn" label="Color scheme for figure. see http://matplotlib.org/examples/color/colormaps_reference.html for choices [default: YlGn]" 
                    name="color_scheme" optional="True" type="text"/>
                <param default="5" label="Width of the figure in inches [default: 5]" 
                    name="width" optional="True" type="text"/>
                <param default="5" label="Height of the figure in inches [default: 5]" 
                    name="height" optional="True" type="text"/>
                <param label="Resolution of the figure in dots per inch [default: 
                    value of savefig.dpi in matplotlibrc file]" name="dpi" 
                    optional="True" type="text"/>
                <param label="Observation metadata category to plot [default: taxonomy]" 
                    name="obs_md_category" optional="True" type="data"/>
                <param label="The level of observation metadata to plot for hierarchical 
                    metadata [default: lowest level]" name="obs_md_level" optional="True" 
                    type="data"/>
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="pdf" from_work_dir="make_otu_heatmap_output" name="heatmap_OTU" 
            label="heatmap_OTU.pdf"/>
    </outputs>

    <tests>
        <test>
        </test>
    </tests>

    <help><![CDATA[

**What it does**

This script visualizes an OTU table as a heatmap where each row corresponds to an 
OTU and each column corresponds to a sample. The higher the relative abundance of 
an OTU in a sample, the more intense the color at the corresponsing position in 
the heatmap. By default, the OTUs (rows) will be clustered by UPGMA hierarchical 
clustering, and the samples (columns) will be presented in the order in which 
they appear in the OTU table. Alternatively, the user may supply a tree to sort 
the OTUs (rows) or samples (columns), or both. The user may also pass in a mapping 
file for sorting samples. If the user passes in a mapping file and a metadata 
category, samples (columns) will be grouped by category value and subsequently 
clustered within each group.
A single output file is created containing the heatmap of the OTU table (a PDF 
file by default).
    ]]>
    </help>

    <citations>
        <expand macro="citations" />
    </citations>
</tool>