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1 <?xml version="1.0" encoding="UTF-8" ?>
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2 <tool id="mda_heatmap_gen" name="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</description>
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8 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc"
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9 "matrix_files|path|$inputmatrix|name|datalayer|summary_method|$summarymethod"
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10 "row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|0|data_type|labels"
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11 "col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|0|data_type|labels"
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12 #for $op in $operations
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13 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cat}'
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14 #end for
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15 'output_location|$output'
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16 </command>
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17 <stdio>
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18 <exit_code range="1:" level="fatal" />
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19 </stdio>
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20 <inputs>
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21 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data." />
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22 <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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23 <sanitizer>
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24 <valid>
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25 <add preset="string.printable"/>
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26 <remove value="""/>
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27 <remove value="'"/>
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28 <remove value=" "/>
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29 </valid>
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30 </sanitizer>
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31 <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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32 <sanitizer>
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33 <valid>
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34 <add preset="string.printable"/>
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35 <add value="string.letters"/>
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36 <add value="string.digits"/>
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37 <add value="-"/>
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38 <add value="_"/>
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39 <remove value="""/>
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40 <remove value="'"/>
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41 <remove value=" "/>
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42 </valid>
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43 </sanitizer>
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44 <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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45 <option value="average">Average</option>
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46 <option value="sample">Sample</option>
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47 <option value="mode">Mode</option>
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48 </param>
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49 <conditional name="d_rows">
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50 <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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51 <option value="Hierarchical">Hierarchical Clustering</option>
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52 <option value="Original">Original Order</option>
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53 <option value="Random">Random</option>
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54 </param>
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55 <when value="Hierarchical">
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56 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows">
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57 <option value="euclidean">Euclidean</option>
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58 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
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59 <option value="manhattan">Manhattan</option>
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60 <option value="maximum">Maximum</option>
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61 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
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62 <option value="minkowski">Minkowski</option>
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63 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
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64 </param>
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65 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
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66 <option value="average">Average Linkage</option>
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67 <option value="complete">Complete Linkage</option>
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68 <option value="single">Single Linkage</option>
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69 <option value="ward" selected="true">Ward</option>
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70 <option value="mcquitty">Mcquitty</option>
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71 <!-- <option value="median">Median</option> ** breaks dendrogram
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72 <option value="centroid">Centroid</option> ** breaks dendrogram -->
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73 </param>
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74 </when>
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75 <when value="Original">
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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 </when>
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79 <when value="Random">
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80 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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81 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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82 </when>
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83 </conditional>
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84 <conditional name="d_cols">
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85 <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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86 <option value="Hierarchical">Hierarchical Clustering</option>
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87 <option value="Original">Original Order</option>
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88 <option value="Random">Random</option>
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89 </param>
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90 <when value="Hierarchical">
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91 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns">
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92 <option value="euclidean">Euclidean</option>
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93 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
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94 <option value="manhattan">Manhattan</option>
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95 <option value="maximum">Maximum</option>
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96 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
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97 <option value="minkowski">Minkowski</option>
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98 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
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99 </param>
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100 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
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101 <option value="average">Average Linkage</option>
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102 <option value="complete">Complete Linkage</option>
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103 <option value="single">Single Linkage</option>
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104 <option value="ward" selected="true">Ward</option>
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105 <option value="mcquitty">Mcquitty</option>
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106 <!-- <option value="median">Median</option> ** breaks dendrogram
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107 <option value="centroid">Centroid</option> ** breaks dendrogram -->
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108 </param>
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109 </when>
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110 <when value="Original">
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111 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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112 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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113 </when>
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114 <when value="Random">
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115 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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116 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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117 </when>
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118 </conditional>
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119 <repeat name="operations" title="Covariate Bars">
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120 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
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121 <sanitizer>
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122 <valid>
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123 <add preset="string.printable"/>
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124 <remove value="""/>
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125 <remove value="'"/>
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126 <remove value=" "/>
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127 </valid>
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128 </sanitizer>
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129 </param>
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130 <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."/>
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131 <param name="cat" type="select" label="Axis Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
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132 <option value="row_discrete" >Row Categorical</option>
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133 <option value="row_continuous" >Row Continuous</option>
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134 <option value="column_discrete" >Column Categorical</option>
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135 <option value="column_continuous" >Column Continuous</option>
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136 </param>
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137 </repeat>
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138 </inputs>
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139 <outputs>
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140 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
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141 </outputs>
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142 <tests>
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143 <test>
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144 <param name="inputmatrix" value="400x400.txt" />
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145 <param name="hmname" value="testRun" />
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146 <param name="$hmdesc" value="validateTool" />
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147 <param name="summarymethod" value="Average" />
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148 <param name="rowOrderMethod" value="Hierarchical" />
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149 <param name="rowDistanceMeasure" value="Manhattan" />
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150 <param name="rowAgglomerationMethod" value="Ward" />
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151 <param name="columnOrderMethod" value="Hierarchical" />
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152 <param name="columnDistanceMeasure" value="Manhattan" />
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153 <param name="columnAgglomerationMethod" value="Ward" />
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154 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
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155
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156 </test>
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157 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
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158 </tests>
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159 </tool>
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