annotate plotheatmap.xml @ 0:bd8fd161908b draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/plotheatmap commit 7e9d6b283879b45d5fe673767668c06104d31609-dirty

<tool id="plotheatmap" name="plotHeatmap" version="1.0">
    <description>Plot heatmap</description>
    <requirements>
        <requirement type="package" version="1.34.0">bioconductor-preprocesscore</requirement>
        <requirement type="package" version="3.0.1">r-gplots</requirement>
    </requirements>
    <command detect_errors="aggressive"><![CDATA[
Rscript '$__tool_directory__/script.R'
'$count_matrix'
'$stats_matrix'
$filter.log_fc
$filter.log_cpm
$filter.pvalue
$filter.fdr
$heatmap.cluster_row
$heatmap.cluster_col
$heatmap.hclust_method
$plotparm.col_marg
$plotparm.row_marg
$plotparm.pdf_width
$plotparm.pdf_height
    ]]></command>
    <inputs>
        <param name="count_matrix" type="data" format="tabular" label="Output dataset 'count_matrix' from tool countMatrixForEdger"/>
        <param name="stats_matrix" type="data" format="tabular" label="Output dataset 'output' from tool edgeR"/>
        <section name="filter" title="Filtering parameters" expanded="true">
            <param name="log_fc" type="float" value="0.5" label="A log FC threshold"/>
            <param name="log_cpm" type="float" value="0.5" label="A log CPM threshold"/>
            <param name="pvalue" type="float" min="0" max="1" value="0.5" label="A p-value threshold"/>
            <param name="fdr" type="float" min="0" max="1" value="0.5" label="An FDR threshold"/>
        </section>
        <section name="heatmap" title="Heatmap parameters">
            <param name="cluster_row" type="boolean" truevalue="Yes" falsevalue="No" checked="true" label="Determines if the row dendrogram should be reordered"/>
            <param name="cluster_col" type="boolean" truevalue="Yes" falsevalue="No" label="Determines if the column dendrogram should be reordered"/>
            <param name="hclust_method" type="select" label="Hierarchical clustering method">
                <option value="ward.D">ward.D</option>
                <option value="ward.D2">ward.D2</option>
                <option value="single">single</option>
                <option value="complete">complete</option>
                <option value="average" selected="true">average</option>
                <option value="mcquitty">mcquitty</option>
                <option value="median">median</option>
                <option value="centroid">centroid</option>
            </param>
        </section>
        <section name="plotparm" title="Plot parameters">
            <param name="col_marg" type="float" value="7" label="Margins for column names"/>
            <param name="row_marg" type="float" value="8" label="Margins for row names"/>
            <param name="pdf_width" type="float" value="7" label="Width of the graphics region in inches (pdf width)"/>
            <param name="pdf_height" type="float" value="7" label="Height of the graphics region in inches (pdf height)"/>
        </section>
    </inputs>
    <outputs>
        <data name="haetamappdf" format="pdf" from_work_dir="heatmap.pdf"/>
    </outputs>
    <tests>
        <test>
            <param name="count_matrix" value="count.matrix"/>
            <param name="stats_matrix" value="stats.data"/>
            <param name="log_fc" value="1"/>
            <param name="log_cpm" value="2"/>
            <param name="pvalue" value="0.05"/>
            <param name="fdr" value="0.1"/>
            <output name="haetamappdf" file="heatmap.pdf" ftype="pdf" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

It takes a list of genes based on set filtering criteria and draws them on heatmap.

**Example**

The following filtering options:
A log FC threshold = 0.5
A log CPM threshold = 0.5
A p-value threshold = 0.05
An FDR threshold = 0.1
mean that you select genes whose values in output table from edgeR are:
* absolute value of log FC is greater than or equal to 0.5
* log CPM is greater than or equal to 0.5
* p-value is less than or equal to 0.05
* FDR is less than or equal to 0.1
    ]]></help>
    <citations>
    </citations>
</tool>