view heatmap2.xml @ 12:c1cb330e162e draft

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<tool id="heatmap2" name="heatmap2" version="0.0.3">
    <requirements>
        <requirement type="package">r-getopt</requirement>
        <requirement type="package">r-rcolorbrewer</requirement>
        <requirement type="package">r-gplots</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        Rscript ${__tool_directory__}/heatmap2.R --input "$input1" --title "$title" 
        --key "$key" --colorscheme "$coloring.colorscheme" --cluster "$clustering.cluster"
        --transform "$transformation.transform" --labels "$label.labels" --scale "$scaling:scale"
        --output "Rplot.pdf"

    ]]></command>
    <inputs>
        <param name="input1" type="data" format="tabular" label="Input should have column headers - these will be the columns that are plotted"/>
        <param name="title" size="30" type="text" format="txt" label="Plot title"/> 
        <param name="key" size="30" type="text" format="txt" label="key title"/> 
        <conditional name="transformation">
            <param name="transform" type="select" label="Advanced - log transformation">
              <option value="none">Plot the data as it is</option>
              <option value="log2">Log2(value) transform my data</option>
              <option value="log2plus1">Log2(value+1) transform my data</option>
              <option value="log10">Log10(value) transform my data</option>
              <option value="log10plus1">Log10(value+1) transform my data</option>
            </param>
        </conditional>
        <conditional name="clustering">
            <param name="cluster" type="select" label="Clustering of data" >
                <option value="Default" selected="True">Cluster my data</option>
                <option value="Defined">Do not cluster my data</option>
            </param>
        </conditional>
        <conditional name="label">
            <param name="labels" type="select" label="Labeling columns and rows" >
                <option value="Both" selected="True">Label my columns and rows</option>
                <option value="rows">Label rows and not columns</option>
                <option value="columns">Label columns and not rows</option>
                <option value="none">Do not label rows or columns</option>
            </param>
        </conditional>
        <conditional name="coloring">
            <param name="colorscheme" type="select" label="Coloring groups" >
                <option value="whrd" selected="True">White to red</option>
                <option value="whblu">White to blue</option>
                <option value="blwhre">Blue to white to red</option>
            </param>
        </conditional>
        <conditional name="scaling">
            <param name="scale" type="select" label="Coloring groups" >
                <option value="none" selected="True">Do not scale my data</option>
                <option value="row">Scale my data by row</option>
                <option value="column">Scale my data by column</option>
            </param>
        </conditional>
    </inputs>
    <outputs>
        <!-- <data name="output1" format="png" from_work_dir="Rplot.png"/> -->
        <data name="output1" format="pdf" from_work_dir="Rplot.pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input.txt"/>
            <output name="output1" file="Rplot.pdf"/>
        </test>
    </tests>
    <help><![CDATA[
This tool will generate a clustered heatmap of your data. More customization options will be added, for now the heatmap uses a red coloring scheme and clustering is performed using the "maximum" similarity measure and the "complete" hierarchical clustering measure. 

Input data should have row labels in the first column and column labels. For example, the row labels (the first column) should represent gene IDs and the column labels should represent sample IDs. 

This wrapper employs the heatmap.2 function of R.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{renameTODO,
  author = {TODO, FirstTODO},
  year = {TODO},
  title = {TODO},
  url = {under construction},
}</citation>
    </citations>
</tool>