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1 <?xml version='1.1' encoding='utf-8'?>
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2 <tool id="Matrix_Manipulation" name="Matrix Manipulation" version="1.2.4">
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3 <description> Data manipulation before heatmap creation</description>
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4
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5 <command interpreter="bash" detect_errors="aggressive">
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6 $__tool_directory__/Matrix_Manipulation.sh '$__tool_directory__' '${manipulation.option}' '$p_input' '$output_file'
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7 '${manipulation.extra.choice}' '${manipulation.extra.thresh}' '${manipulation.extra.axis}'
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8 '${manipulation.extra.transpose}' '${manipulation.extra.input2}' '${manipulation.extra.offsetvalue}' '${manipulation.extra.scalevalue}'
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9
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10 </command>
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11
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12 <inputs>
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13 <param name="p_input" type="data" format="tabular" label="Input Matrix" />
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14 <conditional name="manipulation">
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15 <param name="option" type="select" label="Choose Manipulation Method">
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16 <option value="Matrix_Validations">Missing or Invalid Data</option>
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17 <option value="Matrix_Filters">Filter Data</option>
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18 <option value="Matrix_Transformations">Transform Data</option>
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19 <option value="Matrix_Multiply">Multiply or Correlate Matrices</option>
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20 <!-- <option value="Matrix_Statistics">View metadata about Heat Map Matrix</option> -->
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21 <!-- <option value="Split_ExcelTabs_IntoFiles">Split Excel tabs into separate tab delimited files</option> -->
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22 </param>
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23
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24
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25 <when value="Matrix_Validations">
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26 <conditional name="extra">
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27 <param name="choice" type="select" label="Replace Invalid Value with:">
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28 <option value="Mean">Mean</option>
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29 <option value="Zero">Zero</option>
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30 </param>
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31 <when value="Mean">
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32 <param name="axis" type="select" label="Choose Axis:">
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33 <option value="Row">Row</option>
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34 <option value="Column">Column</option>
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35 </param>
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36
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37 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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38 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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39 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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40 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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41 <param name="input2" type="data" hidden="true" value="$input1" />
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42 </when>
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43 <when value="Zero">
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44 <param name="axis" type="text" size="10" hidden="true" value="Row"/>
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45
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46 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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47 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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48 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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49 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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50 <param name="input2" type="data" hidden="true" value="$input1" />
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51 </when>
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52 </conditional>
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53 </when>
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54
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55
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56
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57 <when value="Matrix_Filters">
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58 <conditional name="extra">
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59 <param name="choice" type="select" label="Filter Criteria:">
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60 <option value="LowerLimit">Remove row/column if any cell is less than threshold value</option>
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61 <option value="UpperLimit">Remove row/column if any cell is greater than threshold value</option>
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62 <option value="NANlimit">Remove row/column if number of invalid cells exceeds threshold value </option>
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63 <option value="NANpercent">Remove row/column if invalid cells exceeds threshold percent</option>
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64 <!-- <option value="VarianceValue">Remove row/column if Variance is below threshold value</option> -->
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65 <option value="VarianceCount">Remove row/column if Variance is not in top row/column count</option>
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66 <option value="VariancePercent">Remove row/column if Variance is not in top percent</option>
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67 <!-- <option value="MADcount">Remove row/column if Median Absolute Deviation (MAD) is not in top row/column count</option>
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68 <option value="MADpercent">Remove row/column if Median Absolute Deviation (MAD) is not in top percent</option> -->
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69 <!-- <option value="Covariance">Remove row/column if covariance exceeds threshold value</option>
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70 <option value="Median">Remove row/column if Median is less than threshold value</option>
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71 <option value="MADvalue">Remove row/column if Median Absolute Deviation (MAD) is below threshold value</option>
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72 <option value="Mean">Remove row/column if Mean is less than threshold value</option>
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73 <option value="Quantile">Remove row/column if less than Quantile_Cutoff</option>
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74 <option value="GeneList">Keep only these genes</option>
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75 <option value="Histogram">View filter histogram</option>
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76 -->
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77 </param>
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78 <when value="LowerLimit">
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79 <param name="thresh" type="float" size="5" value="0.01" label="Absolute minimum value" help="Lowest value allowed or row/col removed."/>
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80 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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81 <option value="Row">Row</option>
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82 <option value="Column">Column</option>
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83 </param>
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84
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85 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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86 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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87 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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88 <param name="input2" type="data" hidden="true" value="$input1" />
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89 </when>
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90 <when value="UpperLimit">
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91 <param name="thresh" type="float" size="5" value="0.9" label="Absolute maximum value" help="Highest value allowed or row/col removed."/>
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92 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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93 <option value="Row">Row</option>
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94 <option value="Column">Column</option>
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95 </param>
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96
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97 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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98 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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99 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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100 <param name="input2" type="data" hidden="true" value="$input1" />
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101 </when>
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102 <when value="NANlimit">
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103 <param name="thresh" type="integer" size="5" value="50" label="Maximum number NANs" help="More NANs per row/col removed."/>
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104 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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105 <option value="Row">Row</option>
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106 <option value="Column">Column</option>
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107 </param>
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108
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109 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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110 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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111 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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112 <param name="input2" type="data" hidden="true" value="$input1" />
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113 </when>
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114 <when value="NANpercent">
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115 <param name="thresh" type="integer" size="5" value="20" label="Percent maximum" help="Above percent rows/cols removed."/>
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116 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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117 <option value="Row">Row</option>
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118 <option value="Column">Column</option>
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119 </param>
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120
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121 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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122 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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123 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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124 <param name="input2" type="data" hidden="true" value="$input1" />
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125 </when>
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126 <when value="VariancePercent">
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127 <param name="thresh" type="integer" size="5" value="90" label="Percentile minimum" help="Below percentile rows/cols removed."/>
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128 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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129 <option value="Row">Row</option>
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130 <option value="Column">Column</option>
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131 </param>
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132
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133 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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134 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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135 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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136 <param name="input2" type="data" hidden="true" value="$input1" />
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137 </when>
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138 <when value="VarianceCount">
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139 <param name="thresh" type="integer" size="5" value="10" label="Number minimum" help="Below threshold rows/cols removed."/>
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140 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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141 <option value="Row">Row</option>
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142 <option value="Column">Column</option>
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143 </param>
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144
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145 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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146 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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147 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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148 <param name="input2" type="data" hidden="true" value="$input1" />
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149 </when>
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150 <when value="MADpercent">
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151 <param name="thresh" type="integer" size="5" value="90" label="Percentile minimum" help="Below percentile rows/cols removed."/>
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152 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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153 <option value="Row">Row</option>
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154 <option value="Column">Column</option>
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155 </param>
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156
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157 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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158 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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159 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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160 <param name="input2" type="data" hidden="true" value="$input1" />
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161 </when>
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162 <when value="MADcount">
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163 <param name="thresh" type="integer" size="5" value="10" label="Number minimum" help="Below threshold rows/cols removed."/>
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164 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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165 <option value="Row">Row</option>
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166 <option value="Column">Column</option>
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167 </param>
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168
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169 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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170 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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171 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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172 <param name="input2" type="data" hidden="true" value="$input1" />
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173 </when>
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174 </conditional>
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175 </when>
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176
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177
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178
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179 <when value="Matrix_Transformations">
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180 <conditional name="extra">
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181 <param name="choice" type="select" label="Choose Normalization Method">
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182 <option value="ln_normalization">Log2 Normalization</option>
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183 <option value="log_normalization">Log10 Normalization</option>
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184 <option value="mean_center_normalization">Mean Centered Normalization</option>
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185 <option value="median_center_normalization">Median Centered Normalization</option>
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186 <option value="z_score_normalization">Z-Score Normalization</option>
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187 <option value="add_offset">Add Offset Value</option>
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188 <option value="scale">Scale by Multiple</option>
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189 <option value="divide_by_sum">Divide by Sum</option>
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190 <option value="transpose">Matrix Transpose</option>
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191 </param>
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192 <when value="add_offset">
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193 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Add value to each Matrix element."/>
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194 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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195 <param name="axis" type="text" size="10" hidden="true" value="Row"/>
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196
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197 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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198 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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199 <param name="input2" type="data" hidden="true" value="$input1" />
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200 </when>
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201 <when value="scale">
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202 <param name="scalevalue" type="text" size="10" value="1.0" label="Matrix Value scaling" help="multiply value with each Matrix element."/>
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203 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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204 <param name="axis" type="text" size="10" hidden="true" value="Row"/>
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205
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206 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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207 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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208 <param name="input2" type="data" hidden="true" value="$input1" />
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209 </when>
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210 <when value="ln_normalization">
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211 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log2 for each Matrix element then add offset."/>
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212 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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213 <param name="axis" type="select" label="Choose Axis">
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214 <option value="Row">Row</option>
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215 <option value="Column">Column</option>
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216 </param>
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217
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218 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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219 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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220 <param name="input2" type="data" hidden="true" value="$input1" />
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221 </when>
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222 <when value="log_normalization">
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223 <param name="offsetvalue" type="text" size="10" value="0.0" label="Matrix Values offset" help="Calculate log10 for each Matrix element then add offset."/>
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224 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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225 <param name="axis" type="select" label="Choose Axis">
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226 <option value="Row">Row</option>
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227 <option value="Column">Column</option>
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228 </param>
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229
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230 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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231 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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232 <param name="input2" type="data" hidden="true" value="$input1" />
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233 </when>
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234 <when value="z_score_normalization">
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235 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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236 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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237 <param name="axis" type="select" label="Choose Axis">
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238 <option value="Row">Row</option>
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239 <option value="Column">Column</option>
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240 </param>
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241
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242 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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243 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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244 <param name="input2" type="data" hidden="true" value="$input1" />
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245 </when>
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246 <when value="mean_center_normalization">
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247 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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248 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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249 <param name="axis" type="select" label="Choose Axis">
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250 <option value="Row">Row</option>
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251 <option value="Column">Column</option>
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252 </param>
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253
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254 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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255 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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256 <param name="input2" type="data" hidden="true" value="$input1" />
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257 </when>
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258 <when value="median_center_normalization">
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259 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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260 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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261 <param name="axis" type="select" label="Choose Axis">
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262 <option value="Row">Row</option>
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263 <option value="Column">Column</option>
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264 </param>
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265
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266 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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267 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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268 <param name="input2" type="data" hidden="true" value="$input1" />
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269 </when>
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270 <when value="transpose">
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271 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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272 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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273 <param name="axis" type="text" size="10" hidden="true" value="neither"/>
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274
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275 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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276 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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277 <param name="input2" type="data" hidden="true" value="$input1" />
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278 </when>
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279 <when value="divide_by_sum">
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280 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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281 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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282 <param name="axis" type="select" label="Choose Axis">
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283 <option value="Row">Row</option>
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284 <option value="Column">Column</option>
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285 </param>
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286
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287 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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288 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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289 <param name="input2" type="data" hidden="true" value="$input1" />
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290 </when>
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291 </conditional>
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292 </when>
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293
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294
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295
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296 <when value="Matrix_Multiply">
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297 <conditional name="extra">
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298 <param name="choice" type="select" label="Choose composition type">
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299 <option value="MatrixMultiply">Matrix Multiplication</option>
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300 <option value="Corr2Matrices">Correlate two matrices</option>
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301 <option value="Corr1Matrix">Correlate one matrix with itself</option>
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302 </param>
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303 <when value="MatrixMultiply">
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304 <param name="transpose" type="select" label="transpose matrix?">
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305 <option value="y">Transpose matrix</option>
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306 <option value="n" selected="true">Do Not transpose matrix</option>
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307 </param>
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308 <param name="input2" type="data" format="tabular" label="Second Input Matrix size NxP" />
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309
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310 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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311 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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312 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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313 <param name="axis" type="text" size="10" hidden="true" value="Row"/>
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314 </when>
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315 <when value="Corr2Matrices">
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316 <param name="transpose" type="select" label="transpose matrix?">
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317 <option value="y">Transpose matrix</option>
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318 <option value="n" selected="true">Do Not transpose matrix</option>
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319 </param>
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320 <param name="input2" type="data" format="tabular" label="Second Input Matrix size NxP" />
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321
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322 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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323 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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324 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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325 <param name="axis" type="text" size="10" hidden="true" value="Row"/>
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326 </when>
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327 <when value="Corr1Matrix">
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328 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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329 <param name="input2" type="data" hidden="true" value="$input1" />
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330
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331 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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332 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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333 <param name="thresh" type="float" size="4" value=".05" hidden="true" />
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334 <param name="axis" type="text" size="10" hidden="true" value="Row"/>
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335 </when>
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336 </conditional>
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337 </when>
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338
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339
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340
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341 <when value="Matrix_Statistics">
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342 <conditional name="extra">
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343 <param name="choice" type="select" label="Choose Metric to Filter By">
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344 <option value="Histogram">Plot info about either matrix row/column</option>
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345 </param>
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346 <when value = "Histogram">
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347 <param name="thresh" type="float" size="4" value=".05" label="Filter Threshold (Value above/below row/column will be Removed)" />
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348 <param name="axis" type="select" label="Choose axis to Filter on (Rows or Columns)">
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349 <option value="Row">Row</option>
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350 <option value="Column">Column</option>
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351 </param>
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352
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353 <param name="offsetvalue" type="text" size="10" hidden="true" value="0"/>
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354 <param name="scalevalue" type="text" size="10" hidden="true" value="1.0"/>
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355 <param name="transpose" type="text" size="10" hidden="true" value="n" />
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356 <param name="input2" type="data" hidden="true" value="$input1" />
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357 </when>
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358 </conditional>
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359 </when>
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360
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361
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362
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363
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364
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365
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366
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367
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368 <!-- <when value="Split_ExcelTabs_IntoFiles">
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369 <description>into separate tab delimited files</description>
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370
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371 <param name="input" type="data" format="txt" label="Input Excel.xls or Excel.xlsx file"> </param>
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372
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373 <conditional name="extra">
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374 <param name="choice" type="select" label="Select tab" help="Select tab position or name">
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375 <option value="tab_number">Tab number</option>
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376 </param>
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377
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378 '$extra.tabname'
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379 <option value="tab_name">Tab name</option>
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380 <option value="all">All tabs in file</option>
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381 <option value="1">First tab only</option>
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382 </param>
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383 <when value="tab_name">
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384 <param name="tabname" type="text" size="20" value="" label="Tab Name" help="Spreadsheet Tab Name">
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385 </param>
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386 </when>
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387
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388 <when value="tab_number">
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389 <param name="tabnumber" type="text" size="2" value="1" label="Tab position" help="Integer Tab position from left">
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390 </param>
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391 </when>
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392 </conditional>
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393
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394 <outputs>
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395 <data name="output_file" format="tabular" label="Output File Name" help="Name based on Input file name and tab name"/>
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396 </outputs>
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397 </when> -->
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398
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399
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400
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401 </conditional>
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402 </inputs>
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403 <outputs>
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404 <data name="output_file" format="tabular" />
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405 </outputs>
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406 </tool> |
