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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="2.0.5">
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3 <description> Create Clustered Heat Maps</description>
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4 <!-- command interpreter="python" detect_errors="aggressive">$__tool_directory__/mad_advanced_heatmap_gen.py 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType -->
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5 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType
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6
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7 "
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8 #for $attr in $hm_attribute
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9 ${attr.attrbute_key}:${attr.attrbute_value};
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10 #end for
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11 "
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12
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13 #for $op in $operations
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14 ${op.class_name}
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15 ${op.repeatinput.file_name}
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16 ${op.cat}
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17 #end for
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18 '$output'
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19 </command>
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20 <stdio>
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21 <exit_code range="1:" level="fatal" />
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22 </stdio>
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23 <inputs>
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24 <param name="inputmatrix" type="data" format="Tabular" label="Input Matrix" />
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25 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>
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26 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>
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27 <param name="summarymethod" type="select" label="Data Summarization Method">
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28 <option value="average">Average</option>
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29 <option value="sample">Sample</option>
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30 <option value="mode">Mode</option>
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31 </param>
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32 <conditional name="d_rows">
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33 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
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34 <option value="Hierarchical">Hierarchical Clustering</option>
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35 <option value="Original">Original Order</option>
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36 <option value="Random">Random</option>
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37 </param>
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38 <when value="Hierarchical">
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39 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
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40 <option value="euclidean">Euclidean</option>
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41 <option value="binary">Binary</option>
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42 <option value="manhattan">Manhattan</option>
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43 <option value="maximum">Maximum</option>
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44 <option value="canberra">Canberra</option>
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45 <option value="minkowski">Minkowski</option>
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46 <option value="correlation">Correlation</option>
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47 </param>
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48 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
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49 <option value="average">Average Linkage</option>
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50 <option value="complete">Complete Linkage</option>
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51 <option value="single">Single Linkage</option>
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52 <option value="ward" selected="true">Ward</option>
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53 <option value="mcquitty">Mcquitty</option>
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54 <option value="median">Median</option>
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55 <option value="centroid">Centroid</option>
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56 </param>
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57 <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" >
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58 <option value="0" selected="true" >None</option>
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59 <option value="2" >2</option>
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60 <option value="3" >3</option>
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61 <option value="4" >4</option>
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62 <option value="5" >5</option>
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63 <option value="6" >6</option>
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64 <option value="7" >7</option>
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65 <option value="8" >8</option>
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66 <option value="9" >9</option>
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67 <option value="10" >10</option>
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68 </param>
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69 </when>
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70 <when value="Original">
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71 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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72 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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73 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
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74 </when>
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75 <when value="Random">
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76 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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77 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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78 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
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79 </when>
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80 </conditional>
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81 <param name="rowDataType" type="select" label="Linkouts to row data type info" >
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82 <option value="labels" selected="true" >None</option>
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83 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
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84 <option value="bio.cbioportal.sampleid" >cBioPortal sample Id</option>
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85 <option value="bio.gene.entrez" >Gene Entrez Id</option>
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86 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
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87 <option value="bio.go" >Gene Ontology (GO) Id</option>
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88 <option value="bio.geo.acc" >GEO Accession Id</option>
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89 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
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90 <option value="bio.mirna" >miRNA Id</option>
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91 <option value="bio.pubmed.search" >Pubmed Search Term</option>
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92 <option value="scholar" >Scholarly term</option>
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93 <option value="bio.protein.uniprotid" >UniProt Id</option>
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94 </param>
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95 <conditional name="d_cols">
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96 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
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97 <option value="Hierarchical">Hierarchical Clustering</option>
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98 <option value="Original">Original Order</option>
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99 <option value="Random">Random</option>
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100 </param>
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101 <when value="Hierarchical">
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102 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
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103 <option value="euclidean">Euclidean</option>
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104 <option value="binary">Binary</option>
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105 <option value="manhattan">Manhattan</option>
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106 <option value="maximum">Maximum</option>
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107 <option value="canberra">Canberra</option>
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108 <option value="minkowski">Minkowski</option>
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109 <option value="correlation">Correlation</option>
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110 </param>
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111 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
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112 <option value="average">Average Linkage</option>
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113 <option value="complete">Complete Linkage</option>
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114 <option value="single">Single Linkage</option>
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115 <option value="ward" selected="true">Ward</option>
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116 <option value="mcquitty">Mcquitty</option>
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117 <option value="median">Median</option>
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118 <option value="centroid">Centroid</option>
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119 </param>
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120 <param name="colDendroCut" type="select" label="Create column categorical covariate bar based on number of top-level dendrogram clusters" >
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121 <option value="0" selected="true" >None</option>
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122 <option value="2" >2</option>
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123 <option value="3" >3</option>
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124 <option value="4" >4</option>
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125 <option value="5" >5</option>
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126 <option value="6" >6</option>
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127 <option value="7" >7</option>
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128 <option value="8" >8</option>
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129 <option value="9" >9</option>
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130 <option value="10" >10</option>
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131 </param>
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132 </when>
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133 <when value="Original">
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134 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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135 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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136 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
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137 </when>
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138 <when value="Random">
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139 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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140 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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141 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
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142 </when>
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143 </conditional>
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144 <param name="colDataType" type="select" label="Linkouts to column data type info" >
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145 <option value="labels" selected="true" >None</option>
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146 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
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147 <option value="bio.cbioportal.sampleid" >cBioPortal sample Id</option>
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148 <option value="bio.gene.entrez" >Gene Entrez Id</option>
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149 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
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150 <option value="bio.go" >Gene Ontology (GO) Id</option>
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151 <option value="bio.geo.acc" >GEO Accession Id</option>
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152 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
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153 <option value="bio.mirna" >miRNA Id</option>
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154 <option value="bio.pubmed.search" >Pubmed Search Term</option>
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155 <option value="scholar" >Scholarly term</option>
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156 <option value="bio.protein.uniprotid" >UniProt Id</option>
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157 </param>
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158 <repeat name="operations" title="Covariate Bars">
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159 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">
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160 <sanitizer invalid_char="_">
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161 <valid initial="none">
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162 <add preset="string.letters"/>
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163 <add preset="string.digits"/>
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164 </valid>
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165 <mapping initial="none">
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166 </mapping>
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167 </sanitizer>
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168 </param>
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169 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>
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170 <param name="cat" type="select" label="Axis Covariate Type">
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171 <option value="row_categorical" >Row Categorical</option>
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172 <option value="row_continuous" >Row Continuous</option>
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173 <option value="column_categorical" >Column Categorical</option>
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174 <option value="column_continuous" >Column Continuous</option>
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175 </param>
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176 </repeat>
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177 <repeat name="hm_attribute" title="Heat Map Attributes">
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178 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attributes json pair-- key ">
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179 <sanitizer invalid_char="_">
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180 <valid initial="">
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181 <add preset="string.letters"/>
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182 <add preset="string.digits"/>
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183 </valid>
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184 <mapping initial="">
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185 </mapping>
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186 </sanitizer>
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187 </param>
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188 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes json pairs -- value ">
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189 <sanitizer invalid_char="_">
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190 <valid initial="">
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191 <add preset="string.letters"/>
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192 <add preset="string.digits"/>
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193 </valid>
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194 <mapping initial="">
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195 </mapping>
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196 </sanitizer>
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197 </param>
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198 </repeat>
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199 </inputs>
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200 <outputs>
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201 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
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202 </outputs>
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203 <tests>
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204 <test>
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205 <param name="inputmatrix" value="400x400.txt" />
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206 <param name="hmname" value="testRun" />
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207 <param name="$hmdesc" value="validateTool" />
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208 <param name="summarymethod" value="Average" />
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209 <param name="rowOrderMethod" value="Hierarchical" />
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210 <param name="rowDistanceMeasure" value="Manhattan" />
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211 <param name="rowAgglomerationMethod" value="Ward" />
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212 <param name="columnOrderMethod" value="Hierarchical" />
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213 <param name="columnDistanceMeasure" value="Manhattan" />
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214 <param name="columnAgglomerationMethod" value="Ward" />
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215 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
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216
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217 </test>
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218 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
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219 </tests>
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220 </tool>
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