annotate metaphlan_hclust_heatmap.xml @ 0:f7353110d18c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan2/ commit 345fb7ef485456ae833be5ad2d2ce4f8765652c8

<tool id="metaphlan_hclust_heatmap" name="Generate heatmap" version="@WRAPPER_VERSION@.0">

    <description>with hierarchical clustering of both samples
and microbial clades for MetaPhlAn2</description>

    <macros>
        <import>metaphlan2_macros.xml</import>
    </macros>

    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <version_command>metaphlan_hclust_heatmap.py -v</version_command>

    <command>
<![CDATA[
        metaphlan_hclust_heatmap.py
            --in '$in'

            #if $output_format == "png"
                --out 'output.png'
            #else if $output_format == "pdf"
                --out 'output.pdf'
            #else if $output_format == "svg"
                --out 'output.svg'
            #end if

            -m '$m'
            -d '$d'
            -f '$f'

            #if $x
                -x '$x'
            #end if
            #if $y
                -y '$y'
            #end if
            --minv '$minv'
            #if $maxv
                --maxv $maxv
            #end if
            --tax_lev '$tax_lev'
            --perc '$perc'
            #if $top
                --top '$top'
            #end if
            --sdend_h '$sdend_h'
            --fdend_w '$fdend_w'
            --cm_h '$cm_h'
            --font_size '$font_size'
            --clust_line_w '$clust_line_w'
            -c '$c'
]]>
    </command>

    <inputs>
        <param argument="--in" type="data" format="tabular,txt" label="Input file of microbial relative abundances" help="This file is typically obtained with merge_metaphlan_tables"/>
        <param name="output_format" type="select" label="Format for the output image">
            <option value="png" selected="true">PNG</option>
            <option value="pdf">PDF</option>
            <option value="svg">SVG</option>
        </param>
        <param argument="-m" type="select" label="Hierarchical clustering method">
            <option value="average" selected="true">Average</option>
            <option value="centroid">Centroid</option>
            <option value="complete">Complete</option>
            <option value="median">Median</option>
            <option value="single">Single</option>
            <option value="ward">Ward</option>
            <option value="weighted">Weighted</option>
        </param>
        <param argument="-d" type="select" label="Distance function for samples">
            <option value="braycurtis" selected="true">braycurtis</option>
            <option value="canberra">canberra</option>
            <option value="chebyshev">chebyshev</option>
            <option value="cityblock">cityblock</option>
            <option value="correlation">correlation</option>
            <option value="cosine">cosine</option>
            <option value="dice">dice</option>
            <option value="euclidean">euclidean</option>
            <option value="hamming">hamming</option>
            <option value="jaccard">jaccard</option>
            <option value="kulsinski">kulsinski</option>
            <option value="mahalanobis">mahalanobis</option>
            <option value="matching">matching</option>
            <option value="minkowski">minkowski</option>
            <option value="rogerstanimoto">rogerstanimoto</option>
            <option value="russellrao">russellrao</option>
            <option value="seuclidean">seuclidean</option>
            <option value="sokalmichener">sokalmichener</option>
            <option value="sokalsneath">sokalsneath</option>
            <option value="sqeuclidean">sqeuclidean</option>
            <option value="wminkowski">wminkowski</option>
            <option value="ward">ward</option>            
            <option value="yule">yule</option>
        </param>
        <param argument="-f" type="select" label="Distance function for microbes">
            <option value="braycurtis">braycurtis</option>
            <option value="canberra">canberra</option>
            <option value="chebyshev">chebyshev</option>
            <option value="cityblock">cityblock</option>
            <option value="correlation" selected="true">correlation</option>
            <option value="cosine">cosine</option>
            <option value="dice">dice</option>
            <option value="euclidean">euclidean</option>
            <option value="hamming">hamming</option>
            <option value="jaccard">jaccard</option>
            <option value="kulsinski">kulsinski</option>
            <option value="mahalanobis">mahalanobis</option>
            <option value="matching">matching</option>
            <option value="minkowski">minkowski</option>
            <option value="rogerstanimoto">rogerstanimoto</option>
            <option value="russellrao">russellrao</option>
            <option value="seuclidean">seuclidean</option>
            <option value="sokalmichener">sokalmichener</option>
            <option value="sokalsneath">sokalsneath</option>
            <option value="sqeuclidean">sqeuclidean</option>
            <option value="wminkowski">wminkowski</option>
            <option value="ward">ward</option>            
            <option value="yule">yule</option>
        </param>
        <param argument="-x" type="integer" optional="True" label="Width of heatmap cells" help="Automatically set, this option should not be necessary unless for very large heatmaps"/>
        <param argument="-y" type="integer" optional="True" label="Height of heatmap cells" help="Automatically set, this option should not be necessary unless for very large heatmaps"/>
        <param argument="--minv" type="float" value="0" label="Minimum value to display" help="Values around 0.001 are also reasonable"/>
        <param argument="--maxv" type="float" optional="True" label="Maximum value to display" help="Default is maximum value present, can be set e.g. to 100 to display the full scale"/>
        <param argument="--tax_lev" type="select" label="Taxonomic level to display">
            <option value="a">All taxonomic levels</option>
            <option value="k">Kingdoms (Bacteria and Archaea) only</option>
            <option value="p">Phyla only</option>
            <option value="c">Classes only</option>
            <option value="o">Orders only</option>
            <option value="f">Families only</option>
            <option value="g">Genera only</option>
            <option value="s" selected="true">Species only</option>
        </param>
        <param argument="--perc" type="integer" value="90" label="Percentile to be used for ordering the microbes"/>
        <param argument="--top" type="integer" optional="True" label="Number of most abundant microbes to display"/>
        <param argument="--sdend_h" type="float" value="0.1" label="Height of the sample dendrogram"/>
        <param argument="--fdend_w" type="float" value="0.1" label="Width of the sample dendrogram"/>
        <param argument="--cm_h" type="float" value="0.03" label="Height of the colormap"/>
        <param argument="--font_size" type="integer" value="7" label="Label font sizes"/>
        <param argument="--clust_line_w" type="float" value="" label="Line width for the dendrograms"/>
        <param argument="-c" type="select" label="Taxonomic level to display">
            <option value="autumn">autumn</option>
            <option value="bbcyr">bbcyr</option>
            <option value="bbcry">bbcry</option>
            <option value="binary">binary</option>
            <option value="Blues">Blues</option>
            <option value="bone">bone</option>
            <option value="BrBG">BrBG</option>
            <option value="brg">brg</option>
            <option value="BuGn">BuGn</option>
            <option value="BuPu">BuPu</option>
            <option value="bwr">bwr</option>
            <option value="cool">cool</option>
            <option value="copper">copper</option>
            <option value="gist_earth">gist_earth</option>
            <option value="gist_ncar">gist_ncar</option>
            <option value="gist_rainbow">gist_rainbow</option>
            <option value="gist_stern">gist_stern</option>
            <option value="GnBu">GnBu</option>
            <option value="gray">gray</option>
            <option value="Greys">Greys</option>
            <option value="hot">hot</option>
            <option value="hsv">hsv</option>
            <option value="jet" selected="true">jet</option>
            <option value="OrRd">OrRd</option>
            <option value="Oranges">Oranges</option>
            <option value="PRGn">PRGn</option>
            <option value="pink">pink</option>
            <option value="PiYG">PiYG</option>
            <option value="PuBu">PuBu</option>
            <option value="PuBuGn">PuBuGn</option>
            <option value="PuOr">PuOr</option>
            <option value="PuRd">PuRd</option>
            <option value="Purples">Purples</option>
            <option value="RdBu">RdBu</option>
            <option value="RdGy">RdGy</option>
            <option value="RdPu">RdPu</option>            
            <option value="RdYlBu">RdYlBu</option>
            <option value="RdYlGn">RdYlGn</option>
            <option value="Reds">Reds</option>
            <option value="seismic">seismic</option>
            <option value="spectral">spectral</option>
            <option value="Spectral">Spectral</option>
            <option value="spring">spring</option>
            <option value="summer">summer</option>
            <option value="terrain">terrain</option>
            <option value="winter">winter</option>
            <option value="YlGn">YlGn</option>
            <option value="YlGnBu">YlGnBu</option>
            <option value="YlOrBr">YlOrBr</option>
            <option value="YlOrRd">YlOrRd</option>
        </param>
    </inputs>

    <outputs>
        <data format="pdf" name="out_pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}">
            <filter>output_format == "pdf"</filter>
        </data>
        <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string}">
            <filter>output_format == "png"</filter>
        </data>
        <data format="svg" name="out_svg" from_work_dir="output.svg" label="${tool.name} on ${on_string}">
            <filter>output_format == "svg"</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="in" value="merged_community_profile.tabular"/>
            <param name="output_format" value="png"/>
            <param name="m" value="average"/>
            <param name="d" value="braycurtis"/>
            <param name="f" value="correlation"/>
            <param name="minv" value="0"/>
            <param name="tax_lev" value="a"/>
            <param name="perc" value="90"/>
            <param name="sdend_h" value="0.1"/>
            <param name="fdend_w" value="0.1"/>
            <param name="cm_h" value="0.03"/>
            <param name="font_size" value="7"/>
            <param name="clust_line_w" value="1"/>
            <param name="c" value="jet"/>
            <output name="out_png" file="heatmap.png" ftype="png" compare="sim_size"/>
        </test>
        <test>
            <param name="in" value="merged_community_profile.tabular"/>
            <param name="output_format" value="pdf"/>
            <param name="m" value="ward"/>
            <param name="d" value="euclidean"/>
            <param name="f" value="euclidean"/>
            <param name="minv" value="0"/>
            <param name="tax_lev" value="a"/>
            <param name="perc" value="90"/>
            <param name="sdend_h" value="0.1"/>
            <param name="fdend_w" value="0.1"/>
            <param name="cm_h" value="0.03"/>
            <param name="font_size" value="7"/>
            <param name="clust_line_w" value="1"/>
            <param name="c" value="pink"/>
            <output name="out_pdf" file="heatmap.pdf" compare="sim_size"/>
        </test>
        <test>
            <param name="in" value="merged_community_profile.tabular"/>
            <param name="output_format" value="svg"/>
            <param name="m" value="complete"/>
            <param name="d" value="hamming"/>
            <param name="f" value="matching"/>
            <param name="minv" value="0"/>
            <param name="tax_lev" value="a"/>
            <param name="perc" value="90"/>
            <param name="sdend_h" value="0.1"/>
            <param name="fdend_w" value="0.1"/>
            <param name="cm_h" value="0.03"/>
            <param name="font_size" value="7"/>
            <param name="clust_line_w" value="1"/>
            <param name="c" value="pink"/>
            <output name="out_svg" file="heatmap.svg" ftype="svg" compare="sim_size"/>
        </test>
    </tests>

    <help><![CDATA[

**What it does**

MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.

This tool generates heatmaps with hierarchical clustering of both samples
and microbial clades. The script can also subsample the number of clades to
display based on the their nth percentile abundance value in each sample

    ]]></help>

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