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1 <?xml version="1.0" encoding="UTF-8" ?>
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2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3">
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3 <requirements>
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4 <requirement type="package" version="3.4.1">r-base</requirement>
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5 <requirement type="package" version="8.0.144">openjdk</requirement>
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6 </requirements>
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7 <description> Create Clustered Heat Maps with Advanced Options</description>
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8 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" "summary_width|$summaryDisplayWidth"
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9 "row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|${d_rows.rowDendroCut}|data_type|$rowDataType|top_items|$rowTopItems|tree_cuts|${d_rows.rcutrows.rowDendroTreeCut}|${d_rows.rcutrows.raddcuts}|dendro_show|${d_rows.rowDendroShow}|dendro_height|${d_rows.rowDendroHeight}"
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10 "col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|${d_cols.colDendroCut}|data_type|$colDataType|top_items|$colTopItems|tree_cuts|${d_cols.ccutrows.colDendroTreeCut}|${d_cols.ccutrows.caddcuts}|dendro_show|${d_cols.columnDendroShow}|dendro_height|${d_cols.columnDendroHeight}"
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11 #for $attr in $hm_attribute
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12 'attribute|${attr.attrbute_key}':'${attr.attrbute_value}'
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13 #end for
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14 #for $mx in $matrices
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15 'matrix_files|path|$mx.dataLayer|name|${mx.dataLayerName}|summary_method|${mx.summarymethod}|selection_color|${mx.dataLayerSelectionColor}|cuts_color|${mx.dataLayerCutsColor}|grid_color|${mx.dataLayerGridColor}|grid_show|${mx.dataLayerGridShow}|${mx.colorsBreaks.setColorsBreaks}|${mx.colorsBreaks.matrixColor1}|${mx.colorsBreaks.matrixColor2}|${mx.colorsBreaks.matrixColor3}|${mx.colorsBreaks.matrixBreak1}|${mx.colorsBreaks.matrixBreak2}|${mx.colorsBreaks.matrixBreak3}|${mx.colorsBreaks.missingColor}'
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16 #end for
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17 #for $op in $operations
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18 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cattype.cat}|bar_type|${op.cattype.scatbar.bartype}|height|${op.classHeight}|fg_color|${op.cattype.scatbar.fg_color}|bg_color|${op.cattype.scatbar.bg_color}'
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19 #end for
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20 'output_location|$output'
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21 </command>
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22 <stdio>
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23 <exit_code range="1:" level="fatal" />
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24 </stdio>
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25 <inputs>
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26 <repeat name="matrices" title="Heat Map Matrices">
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27 <param name="dataLayer" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/>
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28 <param name="dataLayerName" size="40" type="text" value="Data_Layer_name" label="Data Layer Name" help="Name for data layer (no spaces).">
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29 <sanitizer>
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30 <valid>
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31 <add preset="string.printable"/>
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32 <remove value="""/>
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33 <remove value="'"/>
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34 <remove value=" "/>
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35 </valid>
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36 </sanitizer>
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37 </param>
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38 <param name="summarymethod" type="select" label="Data Summarization Method" help="For large matrices, the selected method is used to aggregate data values in the summary view.">
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39 <option value="average">Average</option>
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40 <option value="sample">Sample</option>
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41 <option value="mode">Mode</option>
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42 </param>
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43 <conditional name="colorsBreaks">
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44 <param name="setColorsBreaks" type="select" label="Colors and Breakpoints" help="Select whether to set your own colors and breakpoints or use default values.">
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45 <option value="none">Use System Generated Colors and Breakpoints</option>
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46 <option value="defined">Define Your Own Colors and Breakpoints</option>
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47 </param>
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48 <when value="none">
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49 <param name="matrixColor1" type="text" size="0" hidden="true" value="0"/>
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50 <param name="matrixBreak1" type="text" size="0" hidden="true" value="0"/>
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51 <param name="matrixColor2" type="text" size="0" hidden="true" value="0"/>
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52 <param name="matrixBreak2" type="text" size="0" hidden="true" value="0"/>
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53 <param name="matrixColor3" type="text" size="0" hidden="true" value="0"/>
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54 <param name="matrixBreak3" type="text" size="0" hidden="true" value="0"/>
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55 <param name="missingColor" type="text" size="0" hidden="true" value="0"/>
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56 </when>
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57 <when value="defined">
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58 <param name="matrixColor1" type="color" label="Color for Breakpoint One" value="#ff0000"/>
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59 <param name="matrixBreak1" type="text" label="Value for Breakpoint One" value="-1"/>
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60 <param name="matrixColor2" type="color" label="Color for Breakpoint Two" value="#ffffff"/>
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61 <param name="matrixBreak2" type="text" label="Value for Breakpoint Two" value="0"/>
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62 <param name="matrixColor3" type="color" label="Color for Breakpoint Three" value="#0000ff"/>
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63 <param name="matrixBreak3" type="text" label="Value for Breakpoint Three" value="1"/>
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64 <param name="missingColor" type="color" label="Color for Missing Values" value="#000000"/>
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65 </when>
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66 </conditional>
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67 <param name="dataLayerSelectionColor" type="color" label="Color for selection box" value="#00ff38"/>
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68 <param name="dataLayerCutsColor" type="color" label="Color for Heat Map Gaps" value="#ffffff"/>
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69 <param name="dataLayerGridColor" type="color" label="Color for Heat Map Grid" value="#ffffff"/>
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70 <param name="dataLayerGridShow" type="select" label="Show Heat Map Grid">
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71 <option value="Y">Yes</option>
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72 <option value="N">No</option>
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73 </param>
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74 </repeat>
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75 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
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76 <sanitizer>
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77 <valid>
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78 <add preset="string.printable"/>
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79 <remove value="""/>
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80 <remove value="'"/>
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81 <remove value=" "/>
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82 </valid>
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83 </sanitizer>
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84 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="Heat Map Description" help="Longer description of the heat map contents."/>
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85 <sanitizer>
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86 <valid>
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87 <add preset="string.printable"/>
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88 <remove value="""/>
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89 <remove value="'"/>
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90 <remove value=" "/>
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91 </valid>
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92 </sanitizer>
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93 <param name="summaryDisplayWidth" type="select" label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel.">
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94 <option value="50">50%</option>
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95 <option value="10">10%</option>
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96 <option value="20">20%</option>
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97 <option value="30">30%</option>
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98 <option value="40">40%</option>
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99 <option value="60">60%</option>
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100 <option value="70">70%</option>
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101 <option value="80">80%</option>
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102 <option value="90">90%</option>
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103 </param>
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104 <conditional name="d_rows">
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105 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is.">
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106 <option value="Hierarchical">Hierarchical Clustering</option>
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107 <option value="Original">Original Order</option>
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108 <option value="Random">Random</option>
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109 </param>
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110 <when value="Hierarchical">
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111 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows.">
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112 <option value="euclidean">Euclidean</option>
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113 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
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114 <option value="manhattan">Manhattan</option>
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115 <option value="maximum">Maximum</option>
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116 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
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117 <option value="minkowski">Minkowski</option>
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118 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
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119 </param>
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120 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
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121 <option value="average">Average Linkage</option>
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122 <option value="complete">Complete Linkage</option>
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123 <option value="single">Single Linkage</option>
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124 <option value="ward" selected="true">Ward</option>
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125 <option value="mcquitty">Mcquitty</option>
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126 <!-- <option value="median">Median</option> ** breaks dendrogram
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127 <option value="centroid">Centroid</option> ** breaks dendrogram -->
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128 </param>
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129 <param name="rowDendroShow" type="select" label="Show Row Dendrogram" help="For setting the visibility of the row dendrogram.">
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130 <option value="ALL">Summary and Detail</option>
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131 <option value="SUMMARY">Summary Only</option>
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132 <option value="NONE">Hide</option>
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133 </param>
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134 <param name="rowDendroHeight" type="select" label="Row Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
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135 <option value="100">100%</option>
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136 <option value="50">50%</option>
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137 <option value="75">75%</option>
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138 <option value="125">125%</option>
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139 <option value="150">150%</option>
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140 <option value="200">200%</option>
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141 </param>
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142 <param name="rowDendroCut" type="select" label="Row Cluster Covariate Bar" help="To generate a row covariate bar based on clusters, select the number of clusters(classes) to use.">
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143 <option value="0" selected="true" >None</option>
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144 <option value="2" >2</option>
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145 <option value="3" >3</option>
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146 <option value="4" >4</option>
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147 <option value="5" >5</option>
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148 <option value="6" >6</option>
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149 <option value="7" >7</option>
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150 <option value="8" >8</option>
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151 <option value="9" >9</option>
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152 <option value="10" >10</option>
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153 </param>
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154 <conditional name="rcutrows">
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155 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
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156 <option value="none">None</option>
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157 <option value="treecuts">Cluster-Based Gaps</option>
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158 <option value="positional">Fixed Gaps</option>
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159 </param>
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160 <when value="none">
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161 <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
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162 </when>
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163 <when value="treecuts">
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164 <param name="rowDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters." >
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165 <option value="0" selected="true" >None</option>
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166 <option value="2" >2</option>
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167 <option value="3" >3</option>
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168 <option value="4" >4</option>
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169 <option value="5" >5</option>
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170 <option value="6" >6</option>
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171 <option value="7" >7</option>
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172 <option value="8" >8</option>
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173 <option value="9" >9</option>
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174 <option value="10" >10</option>
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175 </param>
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176 </when>
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177 <when value="positional">
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178 <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
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179 </when>
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180 </conditional>
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181 </when>
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182 <when value="Original">
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183 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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184 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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185 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
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186 <conditional name="rcutrows">
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187 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
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188 <option value="none">None</option>
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189 <option value="positional">Fixed Gaps</option>
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190 </param>
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191 <when value="none">
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192 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
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193 </when>
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194 <when value="positional">
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195 <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
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196 </when>
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197 </conditional>
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198 </when>
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199 <when value="Random">
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200 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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201 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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202 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
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203 <conditional name="rcutrows">
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204 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
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205 <option value="none">None</option>
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206 <option value="positional">Fixed Gaps</option>
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207 </param>
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208 <when value="none">
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209 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
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210 </when>
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211 <when value="positional">
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212 <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
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213 </when>
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214 </conditional>
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215 </when>
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216 </conditional>
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217 <param name="rowTopItems" size="100" type="text" value="None" label="Row Top Items" help="A few rows can be labeled in the full summary heat map. To do so provide a comma delimited list of row labels."/>
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218 <param name="rowDataType" type="select" label="Row Label Type" help="Enable label driven link-outs by specifying the type of row labels.">
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219 <option value="labels" selected="true" >None</option>
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220 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
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221 <option value="bio.feature.agilent" >Agilent Id</option>
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222 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
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223 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
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224 <option value="bio.gene.entrez" >Gene Entrez Id</option>
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225 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
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226 <option value="bio.go" >Gene Ontology (GO) Id</option>
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227 <option value="bio.geo.acc" >GEO Accession Id</option>
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228 <option value="bio.probe.illumina" >Illumina Probe Id</option>
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229 <option value="bio.probe.infinium" >Infinium Probe Id</option>
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230 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
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231 <option value="bio.mirna" >miRNA Id</option>
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232 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
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233 <option value="bio.pubmed" >Pubmed Id</option>
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234 <option value="bio.pubmed.search" >Pubmed Search Term</option>
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235 <option value="scholar" >Scholarly term</option>
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236 <option value="bio.gene.unigene" >Unigene CId</option>
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237 <option value="bio.protein.uniprot" >UniProt Id</option>
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238 </param>
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239 <conditional name="d_cols">
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240 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is.">
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241 <option value="Hierarchical">Hierarchical Clustering</option>
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242 <option value="Original">Original Order</option>
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243 <option value="Random">Random</option>
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244 </param>
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245 <when value="Hierarchical">
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246 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns.">
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247 <option value="euclidean">Euclidean</option>
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6
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248 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
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249 <option value="manhattan">Manhattan</option>
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250 <option value="maximum">Maximum</option>
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6
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251 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
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1
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252 <option value="minkowski">Minkowski</option>
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6
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253 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
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1
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254 </param>
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255 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
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256 <option value="average">Average Linkage</option>
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257 <option value="complete">Complete Linkage</option>
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258 <option value="single">Single Linkage</option>
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259 <option value="ward" selected="true">Ward</option>
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260 <option value="mcquitty">Mcquitty</option>
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6
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261 <!-- <option value="median">Median</option> ** breaks dendrogram
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262 <option value="centroid">Centroid</option> ** breaks dendrogram -->
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1
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263 </param>
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6
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264 <param name="columnDendroShow" type="select" label="Show Column Dendrogram" help="For setting the visibility of the column dendrogram.">
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265 <option value="ALL">Summary and Detail</option>
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266 <option value="SUMMARY">Summary Only</option>
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267 <option value="NONE">Hide</option>
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268 </param>
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269 <param name="columnDendroHeight" type="select" label="Column Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
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270 <option value="100">100%</option>
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271 <option value="50">50%</option>
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272 <option value="75">75%</option>
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273 <option value="125">125%</option>
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274 <option value="150">150%</option>
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275 <option value="200">200%</option>
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276 </param>
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277 <param name="colDendroCut" type="select" label="Column Cluster Covariate Bar" help="To generate a column covariate bar based on clusters, select the number of clusters(classes) to use.">
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1
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278 <option value="0" selected="true" >None</option>
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279 <option value="2" >2</option>
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280 <option value="3" >3</option>
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281 <option value="4" >4</option>
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282 <option value="5" >5</option>
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283 <option value="6" >6</option>
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284 <option value="7" >7</option>
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285 <option value="8" >8</option>
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286 <option value="9" >9</option>
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287 <option value="10" >10</option>
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288 </param>
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289 <conditional name="ccutrows">
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290 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
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291 <option value="none">None</option>
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292 <option value="treecuts">Cluster-Based Gaps</option>
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293 <option value="positional">Fixed Gaps</option>
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294 </param>
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295 <when value="none">
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296 <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
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297 </when>
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298 <when value="treecuts">
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299 <param name="colDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters.">
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6
|
300 <option value="0" selected="true" >None</option>
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301 <option value="2" >2</option>
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302 <option value="3" >3</option>
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303 <option value="4" >4</option>
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304 <option value="5" >5</option>
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305 <option value="6" >6</option>
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306 <option value="7" >7</option>
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307 <option value="8" >8</option>
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308 <option value="9" >9</option>
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309 <option value="10" >10</option>
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1
|
310 </param>
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311 </when>
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312 <when value="positional">
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313 <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
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314 </when>
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315 </conditional>
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316 </when>
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317 <when value="Original">
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318 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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319 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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320 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
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321 <conditional name="ccutrows">
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322 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
|
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323 <option value="none">None</option>
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324 <option value="positional">Fixed Gaps</option>
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|
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325 </param>
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326 <when value="none">
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327 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
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328 </when>
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329 <when value="positional">
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330 <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
|
|
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331 </when>
|
|
|
332 </conditional>
|
|
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333 </when>
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334 <when value="Random">
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335 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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|
|
336 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
|
|
|
337 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
|
|
|
338 <conditional name="ccutrows">
|
|
|
339 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
|
|
|
340 <option value="none">None</option>
|
|
|
341 <option value="positional">Fixed Gaps</option>
|
|
|
342 </param>
|
|
|
343 <when value="none">
|
|
|
344 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
|
|
|
345 </when>
|
|
|
346 <when value="positional">
|
|
|
347 <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/>
|
|
|
348 </when>
|
|
|
349 </conditional>
|
|
|
350 </when>
|
|
|
351 </conditional>
|
|
|
352 <param name="colTopItems" size="100" type="text" value="None" label="Column Top Items" help="A few columns can be labeled in the full summary heat map. To do so provide a comma delimited list of column labels."/>
|
|
|
353 <param name="colDataType" type="select" label="Column Label Type" help="Enable label driven link-outs by specifying the type of column labels.">
|
|
|
354 <option value="labels" selected="true" >None</option>
|
|
|
355 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
|
|
|
356 <option value="bio.feature.agilent" >Agilent Id</option>
|
|
|
357 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
|
|
|
358 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
|
|
|
359 <option value="bio.gene.entrez" >Gene Entrez Id</option>
|
|
|
360 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
|
|
|
361 <option value="bio.go" >Gene Ontology (GO) Id</option>
|
|
|
362 <option value="bio.geo.acc" >GEO Accession Id</option>
|
|
|
363 <option value="bio.probe.illumina" >Illumina Probe Id</option>
|
|
|
364 <option value="bio.probe.infinium" >Infinium Probe Id</option>
|
|
|
365 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
|
|
|
366 <option value="bio.mirna" >miRNA Id</option>
|
|
|
367 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
|
|
|
368 <option value="bio.pubmed" >Pubmed Id</option>
|
|
|
369 <option value="bio.pubmed.search" >Pubmed Search Term</option>
|
|
|
370 <option value="scholar" >Scholarly term</option>
|
|
|
371 <option value="bio.gene.unigene" >Unigene CId</option>
|
|
|
372 <option value="bio.protein.uniprot" >UniProt Id</option>
|
|
|
373 </param>
|
|
|
374 <repeat name="operations" title="Covariate Bars">
|
|
2
|
375 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
|
|
|
376 <sanitizer>
|
|
|
377 <valid>
|
|
|
378 <add preset="string.printable"/>
|
|
|
379 <remove value="""/>
|
|
|
380 <remove value="'"/>
|
|
|
381 <remove value=" "/>
|
|
1
|
382 </valid>
|
|
|
383 </sanitizer>
|
|
|
384 </param>
|
|
2
|
385 <param name="repeatinput" type="data" format="Tabular" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/>
|
|
6
|
386 <param name="classHeight" size="10" type="text" value="15" label="Covariate Display Height" help="Set the display height for column covariates and width for row covariates."/>
|
|
1
|
387 <conditional name="cattype">
|
|
|
388 <param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
|
|
6
|
389 <option value="row_discrete" >Row Categorical</option>
|
|
1
|
390 <option value="row_continuous" >Row Continuous</option>
|
|
6
|
391 <option value="column_discrete" >Column Categorical</option>
|
|
1
|
392 <option value="column_continuous" >Column Continuous</option>
|
|
|
393 </param>
|
|
|
394 <when value="row_continuous">
|
|
6
|
395 <conditional name="scatbar">
|
|
|
396 <param name="bartype" type="select" label="Display Type">
|
|
|
397 <option value="color_plot" >Standard</option>
|
|
|
398 <option value="bar_plot" >Bar Plot</option>
|
|
|
399 <option value="scatter_plot" >Scatter Plot</option>
|
|
|
400 </param>
|
|
|
401 <when value="color_plot">
|
|
|
402 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
|
|
|
403 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
|
|
|
404 </when>
|
|
|
405 <when value="bar_plot">
|
|
|
406 <param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
|
|
|
407 <param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
|
|
|
408 </when>
|
|
|
409 <when value="scatter_plot">
|
|
|
410 <param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
|
|
|
411 <param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
|
|
|
412 </when>
|
|
|
413 </conditional>
|
|
1
|
414 </when>
|
|
|
415 <when value="column_continuous">
|
|
6
|
416 <conditional name="scatbar">
|
|
|
417 <param name="bartype" type="select" label="Display Type">
|
|
|
418 <option value="color_plot" >Standard</option>
|
|
|
419 <option value="bar_plot" >Bar Plot</option>
|
|
|
420 <option value="scatter_plot" >Scatter Plot</option>
|
|
|
421 </param>
|
|
|
422 <when value="color_plot">
|
|
|
423 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
|
|
|
424 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
|
|
|
425 </when>
|
|
|
426 <when value="bar_plot">
|
|
|
427 <param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
|
|
|
428 <param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
|
|
|
429 </when>
|
|
|
430 <when value="scatter_plot">
|
|
|
431 <param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
|
|
|
432 <param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
|
|
|
433 </when>
|
|
|
434 </conditional>
|
|
1
|
435 </when>
|
|
6
|
436 <when value="column_discrete">
|
|
|
437 <conditional name="scatbar">
|
|
|
438 <param name="bartype" type="select" hidden="true">
|
|
|
439 <option value="color_plot" >Standard</option>
|
|
|
440 </param>
|
|
|
441 <when value="color_plot">
|
|
|
442 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
|
|
|
443 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
|
|
|
444 </when>
|
|
|
445 </conditional>
|
|
1
|
446 </when>
|
|
6
|
447 <when value="row_discrete">
|
|
|
448 <conditional name="scatbar">
|
|
|
449 <param name="bartype" type="select" hidden="true">
|
|
|
450 <option value="color_plot" >Standard</option>
|
|
|
451 </param>
|
|
|
452 <when value="color_plot">
|
|
|
453 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
|
|
|
454 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
|
|
|
455 </when>
|
|
|
456 </conditional>
|
|
1
|
457 </when>
|
|
|
458 </conditional>
|
|
|
459 </repeat>
|
|
|
460 <repeat name="hm_attribute" title="Heat Map Attributes">
|
|
|
461 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces).">
|
|
|
462 <sanitizer invalid_char="_">
|
|
|
463 <valid initial="">
|
|
|
464 <add preset="string.letters"/>
|
|
|
465 <add preset="string.digits"/>
|
|
|
466 </valid>
|
|
|
467 <mapping initial="">
|
|
|
468 </mapping>
|
|
|
469 </sanitizer>
|
|
|
470 </param>
|
|
|
471 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces).">
|
|
|
472 <sanitizer invalid_char="_">
|
|
|
473 <valid initial="">
|
|
|
474 <add preset="string.letters"/>
|
|
|
475 <add preset="string.digits"/>
|
|
|
476 </valid>
|
|
|
477 <mapping initial="">
|
|
|
478 </mapping>
|
|
|
479 </sanitizer>
|
|
|
480 </param>
|
|
|
481 </repeat>
|
|
|
482 </inputs>
|
|
|
483 <outputs>
|
|
|
484 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
|
|
|
485 </outputs>
|
|
|
486 <tests>
|
|
|
487 <test>
|
|
|
488 <param name="inputmatrix" value="400x400.txt" />
|
|
|
489 <param name="hmname" value="testRun" />
|
|
|
490 <param name="$hmdesc" value="validateTool" />
|
|
|
491 <param name="summarymethod" value="Average" />
|
|
|
492 <param name="rowOrderMethod" value="Hierarchical" />
|
|
|
493 <param name="rowDistanceMeasure" value="Manhattan" />
|
|
|
494 <param name="rowAgglomerationMethod" value="Ward" />
|
|
|
495 <param name="columnOrderMethod" value="Hierarchical" />
|
|
|
496 <param name="columnDistanceMeasure" value="Manhattan" />
|
|
|
497 <param name="columnAgglomerationMethod" value="Ward" />
|
|
|
498 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
|
|
|
499
|
|
|
500 </test>
|
|
|
501 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
|
|
|
502 </tests>
|
|
|
503 </tool>
|
