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1 <tool id="gen_matrix_heatmap" name="Generate Heatmap for Matrix" force_history_refresh="True">
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2 <command interpreter="python">gen.matrix.heatmap.py
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3 -d ${dataset1}
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4 -i ${image_format_cond.image_format}
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5 -t ${output_treeview_format}
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6 -r ${reverse_rows}
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7
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8 #if str($image_format_cond.image_format) == 'png':
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9 -h $report_html
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10 -p ${report_html.files_path}
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11 #end if
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12 #if str($image_format_cond.image_format) == 'pdf':
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13 -h $report_pdf
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14 #end if
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15 #if str($treeview_output) != 'None':
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16 -o ${treeview_output}
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17 #end if
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18
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19 </command>
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20 <inputs>
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21 <param format="tabular" name="dataset1" type="data" label="Data Matrix" help="Provide a tab-delimited file with data to put into a heatmap generate"/>
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22 <conditional name="image_format_cond">
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23 <param name="image_format" type="select" display='radio' label="Image format">
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24 <option value="pdf">PDF</option>
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25 <option value="png" selected='true' >PNG (html wrapper)</option>
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26 </param>
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27 </conditional>
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28 <param name="output_treeview_format" type='select' display="radio" label="Output in TreeView format as well?" help="Specify whether or not to produce files for TreeView">
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29 <option value="no">No</option>
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30 <option value="yes" selected='true' >Yes</option>
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31 </param>
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32 <param name="reverse_rows" type='select' display="radio" label="Reverse Row-order (to make consistent w\TreeView Display)?" help="Specify whether or not to reverse Row-order (to make the heatmap consistent with output from TreeView (reversed otherwise)">
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33 <option value="no" selected='true'>No</option>
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34 <option value="yes">Yes</option>
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35 </param>
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36 </inputs>
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37 <outputs>
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38 <data format="html" name="report_html" label="Heatmap from data matrix (HTML)">
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39 <filter>(image_format_cond['image_format']=="png")</filter>
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40 </data>
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41 <data format="pdf" name="report_pdf" label="Heatmap from data matrix (PDF)">
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42 <filter>(image_format_cond['image_format']=="pdf")</filter>
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43 </data>
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44 <data format="tgz" name="treeview_output" label="Heatmap from data matrix (tgz of TreeView files)">
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45 <filter>(output_treeview_format)=="yes"</filter>
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46 </data>
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47 </outputs>
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48 <help>
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49 .. class:: infomark
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50
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51 **Generate Heatmap for Matrix** - Tool to Generate a simple heatmap for a data matrix
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52 - The tool uses HAC, with euclidean distance. If user wants other options, we recomend using either the:
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53
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54 * Consensus Clustering tool
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55 * Hierarchcical Clustering tool, OR
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56 * Partitition Clusterint tool
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57
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58 **OUTPUT:**
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59 * **Heatmap** in either PDF or PNG format
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60 * **TreeView Files** gzip tarball file of the relevant files (OPTIONAL)
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61
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62 ----
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63
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64 **Parameters**
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65
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66 - **Matrix in tab-delimited format** Tab-delimited file
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67
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68 </help>
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69 </tool>
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