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1 <tool id="secimtools_hierarchical_clustering_heatmap" name="Hierarchical Clustering Heatmap" version="@WRAPPER_VERSION@">
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2 <description>- Calculate means per group and plot a heatmap.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 hierarchical_clustering_heatmap.py
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9 --input $input
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10 --design $design
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11 --uniqID $uniqID
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12 #if $dendogram
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13 --dendogram
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14 #end if
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15 --labels $labels
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16 --fig $fig
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17 ]]></command>
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18 <inputs>
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19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
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20 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
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21 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
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22 <param name="dendogram" type="boolean" value="False" label="Add dendogram on heatmap" help="Select 'Yes' to print a dendogram over the heatmap."/>
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23 <param name="labels" type="select" label="Select to remove labels from plots" multiple="true" display="checkboxes">
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24 <option value="x">X-axis labels</option>
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25 <option value="y">Y-axis labels</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data format="pdf" name="fig" label="${tool.name} on ${on_string}"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="input" value="ST000006_data.tsv"/>
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34 <param name="design" value="ST000006_design.tsv"/>
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35 <param name="uniqID" value="Retention_Index" />
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36 <param name="dendogram" value="True" />
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37 <param name="labels" value="x,y" />
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38 <output name="fig" file="ST000006_hierarchical_clustering_heatmap_figure.pdf" compare="sim_size" delta="10000" />
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42
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43 @TIP_AND_WARNING@
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44
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45 **Tool Description**
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46
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47 This tool generates a hierarchical cluster heatmap from a wide format dataset.
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48 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.
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49
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50 **NOTE:** This script works best with log transformed data that contains no missing data.
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51
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52 --------------------------------------------------------------------------------
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53
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54 **Input**
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55
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56 - Two input datasets are required.
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57
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58 @WIDE@
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59
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60 **NOTE:** The sample IDs must match the sample IDs in the Design File
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61 (below). Extra columns will automatically be ignored.
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62
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63
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64 @METADATA@
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65
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66 **In addition to your datasets, you need to provide:**
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67
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68 **Unique Feature ID**
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69
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70 - The column name in your wide dataset that contains the unique IDs for
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71 your features. In our example dataset you would input *Compound*.
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72
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73 --------------------------------------------------------------------------------
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74
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75 **Output**
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76
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77 A PDF file with a hierarchical cluster heatmap of the data
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78
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79 ]]></help>
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80 <expand macro="citations"/>
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81 </tool>
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