annotate hierarchical_clustering_heatmap.xml @ 1:2e7d47c0b027 draft

"planemo upload for repository https://[e-mail]/repos/malex/secimtools"

<tool id="secimtools_hierarchical_clustering_heatmap" name="Hierarchical Clustering Heatmap" version="@WRAPPER_VERSION@">
    <description>- Calculate means per group and plot a heatmap.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
hierarchical_clustering_heatmap.py
--input $input
--design $design
--uniqID $uniqID
#if $dendogram
    --dendogram
#end if
--labels $labels
--fig $fig
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
        <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
        <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
        <param name="dendogram" type="boolean" value="False" label="Add dendogram on heatmap" help="Select 'Yes' to print a dendogram over the heatmap."/>
        <param name="labels" type="select" label="Select to remove labels from plots" multiple="true" display="checkboxes">
            <option value="x">X-axis labels</option>
            <option value="y">Y-axis labels</option>
        </param>
    </inputs>
    <outputs>
        <data format="pdf" name="fig" label="${tool.name} on ${on_string}"/>
    </outputs>
    <tests>
        <test>
            <param name="input"     value="ST000006_data.tsv"/>
            <param name="design"    value="ST000006_design.tsv"/>
            <param name="uniqID"    value="Retention_Index" />
            <param name="dendogram" value="True" />
            <param name="labels"    value="x,y" />
            <output name="fig"      file="ST000006_hierarchical_clustering_heatmap_figure.pdf" compare="sim_size" delta="10000" />
         </test>
    </tests>
<help><![CDATA[

@TIP_AND_WARNING@

**Tool Description**

This tool generates a hierarchical cluster heatmap from a wide format dataset.
An option to add a hierarchical clustering dendrogram on the top of the heatmap figure is included along with an option to removal plot labels.

**NOTE:** This script works best with log transformed data that contains no missing data.

--------------------------------------------------------------------------------

**Input**

- Two input datasets are required.

	@WIDE@

    **NOTE:** The sample IDs must match the sample IDs in the Design File
    (below). Extra columns will automatically be ignored.


	@METADATA@

**In addition to your datasets, you need to provide:**

**Unique Feature ID**

    - The column name in your wide dataset that contains the unique IDs for
      your features. In our example dataset you would input *Compound*.

--------------------------------------------------------------------------------

**Output**

A PDF file with a hierarchical cluster heatmap of the data

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