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1 <?xml version="1.0" encoding="UTF-8" ?>
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2
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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 </requirements>
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6 <description> Create Clustered Heat Maps with Advanced Options</description>
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7 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh 'advanced' 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__;$__tool_data_path__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems'
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1
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8
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9 "
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10 #for $attr in $hm_attribute
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11 ${attr.attrbute_key}:${attr.attrbute_value};
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12 #end for
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13 "
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14
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15 #for $op in $operations
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16 ${op.class_name}
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17 ${op.repeatinput.file_name}
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18 ${op.cattype.cat}
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19 ${op.cattype.bartype}
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20 #end for
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21 '$output'
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22 </command>
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23 <stdio>
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24 <exit_code range="1:" level="fatal" />
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25 </stdio>
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26 <inputs>
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27 <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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2
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28 <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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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 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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2
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38 <sanitizer>
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39 <valid>
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40 <add preset="string.printable"/>
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41 <remove value="""/>
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42 <remove value="'"/>
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43 <remove value=" "/>
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44 </valid>
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45 </sanitizer>
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46 <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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47 <option value="average">Average</option>
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48 <option value="sample">Sample</option>
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49 <option value="mode">Mode</option>
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50 </param>
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51 <conditional name="d_rows">
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52 <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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53 <option value="Hierarchical">Hierarchical Clustering</option>
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54 <option value="Original">Original Order</option>
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55 <option value="Random">Random</option>
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56 </param>
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57 <when value="Hierarchical">
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58 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows.">
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59 <option value="euclidean">Euclidean</option>
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60 <option value="binary">Binary</option>
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61 <option value="manhattan">Manhattan</option>
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62 <option value="maximum">Maximum</option>
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63 <option value="canberra">Canberra</option>
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64 <option value="minkowski">Minkowski</option>
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65 <option value="correlation">Correlation</option>
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66 </param>
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67 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
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68 <option value="average">Average Linkage</option>
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69 <option value="complete">Complete Linkage</option>
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70 <option value="single">Single Linkage</option>
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71 <option value="ward" selected="true">Ward</option>
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72 <option value="mcquitty">Mcquitty</option>
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73 <option value="median">Median</option>
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74 <option value="centroid">Centroid</option>
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75 </param>
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76 <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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77 <option value="0" selected="true" >None</option>
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78 <option value="2" >2</option>
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79 <option value="3" >3</option>
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80 <option value="4" >4</option>
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81 <option value="5" >5</option>
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82 <option value="6" >6</option>
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83 <option value="7" >7</option>
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84 <option value="8" >8</option>
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85 <option value="9" >9</option>
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86 <option value="10" >10</option>
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87 </param>
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88 <conditional name="rcutrows">
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89 <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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90 <option value="none">None</option>
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91 <option value="treecuts">Cluster-Based Gaps</option>
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92 <option value="positional">Fixed Gaps</option>
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93 </param>
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94 <when value="none">
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95 <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
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96 </when>
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97 <when value="treecuts">
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98 <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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99 <option value="0t" selected="true" >None</option>
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100 <option value="2t" >2</option>
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101 <option value="3t" >3</option>
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102 <option value="4t" >4</option>
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103 <option value="5t" >5</option>
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104 <option value="6t" >6</option>
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105 <option value="7t" >7</option>
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106 <option value="8t" >8</option>
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107 <option value="9t" >9</option>
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108 <option value="10t" >10</option>
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109 </param>
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110 </when>
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111 <when value="positional">
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112 <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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113 </when>
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114 </conditional>
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115 </when>
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116 <when value="Original">
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117 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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118 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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119 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
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120 <conditional name="rcutrows">
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121 <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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122 <option value="none">None</option>
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123 <option value="positional">Fixed Gaps</option>
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124 </param>
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125 <when value="none">
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126 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
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127 </when>
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128 <when value="positional">
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129 <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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130 </when>
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131 </conditional>
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132 </when>
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133 <when value="Random">
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134 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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135 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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136 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
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137 <conditional name="rcutrows">
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138 <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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139 <option value="none">None</option>
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140 <option value="positional">Fixed Gaps</option>
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141 </param>
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142 <when value="none">
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143 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
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144 </when>
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145 <when value="positional">
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146 <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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147 </when>
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148 </conditional>
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149 </when>
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150 </conditional>
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151 <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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152 <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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153 <option value="labels" selected="true" >None</option>
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154 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
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155 <option value="bio.feature.agilent" >Agilent Id</option>
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156 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
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157 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
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158 <option value="bio.gene.entrez" >Gene Entrez Id</option>
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159 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
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160 <option value="bio.go" >Gene Ontology (GO) Id</option>
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161 <option value="bio.geo.acc" >GEO Accession Id</option>
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162 <option value="bio.probe.illumina" >Illumina Probe Id</option>
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163 <option value="bio.probe.infinium" >Infinium Probe Id</option>
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164 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
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165 <option value="bio.mirna" >miRNA Id</option>
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166 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
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167 <option value="bio.pubmed" >Pubmed Id</option>
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168 <option value="bio.pubmed.search" >Pubmed Search Term</option>
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169 <option value="scholar" >Scholarly term</option>
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170 <option value="bio.gene.unigene" >Unigene CId</option>
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171 <option value="bio.protein.uniprot" >UniProt Id</option>
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172 </param>
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173 <conditional name="d_cols">
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174 <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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175 <option value="Hierarchical">Hierarchical Clustering</option>
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176 <option value="Original">Original Order</option>
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177 <option value="Random">Random</option>
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178 </param>
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179 <when value="Hierarchical">
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180 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns.">
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181 <option value="euclidean">Euclidean</option>
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182 <option value="binary">Binary</option>
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183 <option value="manhattan">Manhattan</option>
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184 <option value="maximum">Maximum</option>
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185 <option value="canberra">Canberra</option>
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186 <option value="minkowski">Minkowski</option>
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187 <option value="correlation">Correlation</option>
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188 </param>
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189 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
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190 <option value="average">Average Linkage</option>
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191 <option value="complete">Complete Linkage</option>
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192 <option value="single">Single Linkage</option>
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193 <option value="ward" selected="true">Ward</option>
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194 <option value="mcquitty">Mcquitty</option>
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195 <option value="median">Median</option>
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196 <option value="centroid">Centroid</option>
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197 </param>
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198 <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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199 <option value="0" selected="true" >None</option>
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200 <option value="2" >2</option>
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201 <option value="3" >3</option>
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202 <option value="4" >4</option>
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203 <option value="5" >5</option>
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204 <option value="6" >6</option>
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205 <option value="7" >7</option>
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206 <option value="8" >8</option>
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207 <option value="9" >9</option>
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208 <option value="10" >10</option>
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209 </param>
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210 <conditional name="ccutrows">
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211 <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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212 <option value="none">None</option>
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213 <option value="treecuts">Cluster-Based Gaps</option>
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214 <option value="positional">Fixed Gaps</option>
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215 </param>
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216 <when value="none">
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217 <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
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218 </when>
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219 <when value="treecuts">
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220 <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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221 <option value="0t" selected="true" >None</option>
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222 <option value="2t" >2</option>
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223 <option value="3t" >3</option>
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224 <option value="4t" >4</option>
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225 <option value="5t" >5</option>
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226 <option value="6t" >6</option>
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227 <option value="7t" >7</option>
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228 <option value="8t" >8</option>
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229 <option value="9t" >9</option>
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230 <option value="10t" >10</option>
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231 </param>
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232 </when>
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233 <when value="positional">
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234 <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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235 </when>
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236 </conditional>
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237 </when>
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238 <when value="Original">
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239 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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240 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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241 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
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242 <conditional name="ccutrows">
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243 <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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244 <option value="none">None</option>
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245 <option value="positional">Fixed Gaps</option>
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246 </param>
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247 <when value="none">
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248 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
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249 </when>
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250 <when value="positional">
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251 <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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252 </when>
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253 </conditional>
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254 </when>
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255 <when value="Random">
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256 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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257 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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258 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
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259 <conditional name="ccutrows">
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260 <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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261 <option value="none">None</option>
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262 <option value="positional">Fixed Gaps</option>
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263 </param>
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264 <when value="none">
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265 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
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266 </when>
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267 <when value="positional">
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268 <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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269 </when>
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270 </conditional>
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271 </when>
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272 </conditional>
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273 <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."/>
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274 <param name="colDataType" type="select" label="Column Label Type" help="Enable label driven link-outs by specifying the type of column labels.">
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275 <option value="labels" selected="true" >None</option>
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276 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
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277 <option value="bio.feature.agilent" >Agilent Id</option>
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278 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
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279 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
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280 <option value="bio.gene.entrez" >Gene Entrez Id</option>
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281 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
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282 <option value="bio.go" >Gene Ontology (GO) Id</option>
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283 <option value="bio.geo.acc" >GEO Accession Id</option>
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284 <option value="bio.probe.illumina" >Illumina Probe Id</option>
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285 <option value="bio.probe.infinium" >Infinium Probe Id</option>
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286 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
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287 <option value="bio.mirna" >miRNA Id</option>
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288 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
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289 <option value="bio.pubmed" >Pubmed Id</option>
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290 <option value="bio.pubmed.search" >Pubmed Search Term</option>
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291 <option value="scholar" >Scholarly term</option>
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292 <option value="bio.gene.unigene" >Unigene CId</option>
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293 <option value="bio.protein.uniprot" >UniProt Id</option>
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294 </param>
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295 <repeat name="operations" title="Covariate Bars">
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2
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296 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
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297 <sanitizer>
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298 <valid>
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299 <add preset="string.printable"/>
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300 <remove value="""/>
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301 <remove value="'"/>
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302 <remove value=" "/>
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1
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303 </valid>
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304 </sanitizer>
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305 </param>
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2
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306 <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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1
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307 <conditional name="cattype">
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308 <param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
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309 <option value="row_categorical" >Row Categorical</option>
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310 <option value="row_continuous" >Row Continuous</option>
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311 <option value="column_categorical" >Column Categorical</option>
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312 <option value="column_continuous" >Column Continuous</option>
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313 </param>
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314 <when value="row_continuous">
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315 <param name="bartype" type="select" label="Display Type">
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316 <option value="color_plot" >Standard</option>
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317 <option value="bar_plot" >Bar Plot</option>
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318 <option value="scatter_plot" >Scatter Plot</option>
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319 </param>
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320 </when>
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321 <when value="column_continuous">
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322 <param name="bartype" type="select" label="Display Type">
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323 <option value="color_plot" >Standard</option>
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324 <option value="bar_plot" >Bar Plot</option>
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325 <option value="scatter_plot" >Scatter Plot</option>
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326 </param>
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327 </when>
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328 <when value="column_categorical">
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329 <param name="bartype" type="text" hidden="true" value="color_plot"/>
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330 </when>
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331 <when value="row_categorical">
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332 <param name="bartype" type="text" hidden="true" value="color_plot"/>
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333 </when>
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334 </conditional>
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335 </repeat>
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336 <repeat name="hm_attribute" title="Heat Map Attributes">
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337 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces).">
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338 <sanitizer invalid_char="_">
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339 <valid initial="">
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340 <add preset="string.letters"/>
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341 <add preset="string.digits"/>
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342 </valid>
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343 <mapping initial="">
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344 </mapping>
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345 </sanitizer>
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346 </param>
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347 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces).">
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348 <sanitizer invalid_char="_">
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349 <valid initial="">
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350 <add preset="string.letters"/>
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351 <add preset="string.digits"/>
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352 </valid>
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353 <mapping initial="">
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354 </mapping>
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355 </sanitizer>
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356 </param>
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357 </repeat>
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358 </inputs>
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359 <outputs>
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360 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
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361 </outputs>
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362 <tests>
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363 <test>
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364 <param name="inputmatrix" value="400x400.txt" />
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365 <param name="hmname" value="testRun" />
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366 <param name="$hmdesc" value="validateTool" />
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367 <param name="summarymethod" value="Average" />
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368 <param name="rowOrderMethod" value="Hierarchical" />
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369 <param name="rowDistanceMeasure" value="Manhattan" />
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370 <param name="rowAgglomerationMethod" value="Ward" />
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371 <param name="columnOrderMethod" value="Hierarchical" />
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372 <param name="columnDistanceMeasure" value="Manhattan" />
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373 <param name="columnAgglomerationMethod" value="Ward" />
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374 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
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375
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376 </test>
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377 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
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378 </tests>
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379 </tool>
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