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1 <tool id="cluster_heatmap" name="Generate Heatmap for Clustering Result" force_history_refresh="True">
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2 <command interpreter="python">heatmap.from.cluster.result.py
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3 -d ${dataset1}
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4 -s ${cluster_second_direction_cond.cluster_second_direction}
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5
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6 #if str($cluster_second_direction_cond.cluster_second_direction) == 'prev':
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7 -D ${cluster_second_direction_cond.dataset2}
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8 #end if
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9 -i ${image_format_cond.image_format}
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10 -t ${output_treeview_format}
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11 -r ${reverse_rows}
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12 -k ${plot_kms_cond.plot_kms}
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13 #if str($plot_kms_cond.plot_kms) == 'yes':
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14 -C ${dataset1}
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15 -S ${plot_kms_cond.survial_data}
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16 -M ${plot_kms_cond.mode}
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17 -T "${plot_kms_cond.title}"
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18 -I none
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19 #end if
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20
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21 #if str($image_format_cond.image_format) == 'png':
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22 -h $report_html
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23 -p ${report_html.files_path}
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24 #end if
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25 #if str($image_format_cond.image_format) == 'pdf':
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26 -h $report_pdf
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27 -p ${report_pdf.files_path}
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28 #end if
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29 #if str($treeview_output) != 'None':
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30 -o ${treeview_output}
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31 #end if
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32
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33 </command>
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34 <inputs>
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35 <param format="rdata" name="dataset1" type="data" label="Clustering Classification" help="Cluster result file from CCPLUS, HAC, or PAM"/>
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36 <conditional name="plot_kms_cond">
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37 <param name="plot_kms" type='select' label="Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?" help="NOTE: this only works when the Image Format is PNG. For a PDF of the KM plot, you can use the 'Generate Kaplan-Meiers Plot for Cluster Result' tool">
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38 <option value="yes" >Yes</option>
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39 <option value="no" selected='true'>No</option>
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40 </param>
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41 <when value='yes'>
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42 <param name="survial_data" type="data" format="tabular" label="Clinical Data" help="Specify the clinical data to use for the Kaplan-Meiers Plot (see help)"/>
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43 <param name="mode" type="select" display='radio' label="Report Mode" help="Specify the mode to use when performing Log-Rank tests (see help below)">
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44 <option value="all" selected='true' >All</option>
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45 <option value="one">One</option>
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46 <option value="both">Both</option>
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47 </param>
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48 <param name="title" type="text" label="Title" value="Report"/>
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49 </when>
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50 </conditional>
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51 <conditional name="cluster_second_direction_cond">
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52 <param name="cluster_second_direction" type="select" label="Cluster the second dimension? (e.g. rows if this is a sample cluster)" help="Cluster the 2nd dimension of matrix in the cluster result (see help below)">
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53 <option value="yes">Yes</option>
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54 <option value="no" selected="true">No</option>
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55 <option value="prev">Previous Cluster Result</option>
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56 </param>
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57 <when value="prev">
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58 <param format="rdata" name="dataset2" type="data" label="Previous Cluster result #2 (secondary result, e.g. rows)" help="Cluster result file from CCPLUS, HAC, or PAM"/>
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59 </when>
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60 </conditional>
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61 <conditional name="image_format_cond">
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62 <param name="image_format" type="select" display='radio' label="Image format">
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63 <option value="pdf">PDF</option>
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64 <option value="png" selected='true' >PNG (html wrapper)</option>
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65 </param>
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66 </conditional>
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67 <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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68 <option value="yes" selected='true' >Yes</option>
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69 <option value="no">No</option>
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70 </param>
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71 <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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72 <option value="yes">Yes</option>
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73 <option value="no" selected='true'>No</option>
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74 </param>
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75 </inputs>
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76 <outputs>
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77 <data format="html" name="report_html" label="Heatmap from cluster results (HTML)">
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78 <filter>(image_format_cond['image_format']=="png")</filter>
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79 </data>
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80 <data format="pdf" name="report_pdf" label="Heatmap from cluster results (PDF)">
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81 <filter>(image_format_cond['image_format']=="pdf")</filter>
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82 </data>
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83 <data format="tgz" name="treeview_output" label="Heatmap from cluster results (tgz of TreeView files)">
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84 <filter>(output_treeview_format)=="yes"</filter>
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85 </data>
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86 </outputs>
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87 <help>
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88 .. class:: infomark
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89
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90 **Generate Heatmap for Clustering Result** - Tool to generate a heatmap and dendrogram for a clustering result
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91
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92 **OUTPUT:**
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93 * **Heatmap** in either PDF or PNG format
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94 * **TreeView Files** gzip tarball file of the relevant files (OPTIONAL)
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95
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96 ----
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97
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98 **Parameters**
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99
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100 - **Clustering Classification** Specify the clustering classification (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format).
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101
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102 - **Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?** Specify whether or not to also plot a Kaplan-Meiers Surivial Plot. **NOTE*, the cluster results must be a **SAMPLE** cluster.
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103
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104 - **Cluster the second dimension?** Specify whether or not to cluster the 2nd dimension of matrix in the cluster result. Choice of:
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105 * No
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106 * Yes - Generate a default clustering (HAC with Euclidean distance)
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107 * Previous Cluster Result - MUST specify a previous clustering result
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108
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109 - **IF Cluster the second dimension? is a previous clustering result:**
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110 * **Previous Cluster result #2** Specify the clustering classification for the 2nd dimension (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format).
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111
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112 - **IF Plot Kaplan-Meiers Survival Plot is YES:**
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113 * **Clinical Data** Clinical data to use for the Kaplan-Meiers Plot (must be formated - See the "Format Raw TCGA sample IDs")
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114
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115 * **Report Mode** Mode to use when performing Log-Rank tests **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE)** . Choice of:
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116
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117 * All - All clusters versus each other
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118 * One - One cluster versus a meta-cluster composed of the others. Search performed exhaustively.
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119 * Both - Perform both all-v-all and and one-v-others test; select the choice of K that gives the best
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120
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121 * **Title** - Title to use for Kaplan-Meiers Plot
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122
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123
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124 </help>
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125 </tool>
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