annotate mda_heatmap_gen.xml @ 32:16593e40c2cd draft

Version 2.0.5
author insilico-bob
date Thu, 20 Jul 2017 15:31:06 -0400
parents 5d22d515b470
children 0097750ad7ad
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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="2.0.5">
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3 <description>Create Clustered Heat Maps</description>
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4 <!-- <command interpreter="python" detect_errors="aggressive">$__tool_directory__/mda_heatmap_gen.py 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' 0 0 labels labels 'None'-->
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5 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "Heat_Map_$hmname" "$hmdesc" '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__/' 0 0 labels labels 'None'
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6 #for $op in $operations
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7 ${op.class_name}
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8 ${op.repeatinput.file_name}
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9 ${op.cat}
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10 #end for
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11 '$output'
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12 </command>
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13 <stdio>
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14 <exit_code range="1:" level="fatal" />
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15 </stdio>
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16 <inputs>
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17 <param name="inputmatrix" type="data" format="Tabular" label="Input Matrix" />
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18 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>
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19 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>
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20 <param name="summarymethod" type="select" label="Data Summarization Method">
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21 <option value="average">Average</option>
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22 <option value="sample">Sample</option>
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23 <option value="mode">Mode</option>
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24 </param>
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25 <conditional name="d_rows">
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26 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
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27 <option value="Hierarchical">Hierarchical Clustering</option>
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28 <option value="Original">Original Order</option>
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29 <option value="Random">Random</option>
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30 </param>
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31 <when value="Hierarchical">
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32 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
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33 <option value="euclidean">Euclidean</option>
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34 <option value="binary">Binary</option>
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35 <option value="manhattan">Manhattan</option>
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36 <option value="maximum">Maximum</option>
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37 <option value="canberra">Canberra</option>
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38 <option value="minkowski">Minkowski</option>
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39 <option value="correlation">Correlation</option>
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40 </param>
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41 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
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42 <option value="average">Average Linkage</option>
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43 <option value="complete">Complete Linkage</option>
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44 <option value="single">Single Linkage</option>
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45 <option value="ward" selected="true">Ward</option>
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46 <option value="mcquitty">Mcquitty</option>
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47 <option value="median">Median</option>
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48 <option value="centroid">Centroid</option>
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49 </param>
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50 </when>
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51 <when value="Original">
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52 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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53 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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54 </when>
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55 <when value="Random">
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56 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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57 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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58 </when>
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59 </conditional>
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60 <conditional name="d_cols">
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61 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
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62 <option value="Hierarchical">Hierarchical Clustering</option>
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63 <option value="Original">Original Order</option>
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64 <option value="Random">Random</option>
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65 </param>
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66 <when value="Hierarchical">
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67 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
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68 <option value="euclidean">Euclidean</option>
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69 <option value="binary">Binary</option>
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70 <option value="manhattan">Manhattan</option>
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71 <option value="maximum">Maximum</option>
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72 <option value="canberra">Canberra</option>
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73 <option value="minkowski">Minkowski</option>
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74 <option value="correlation">Correlation</option>
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75 </param>
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76 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
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77 <option value="average">Average Linkage</option>
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78 <option value="complete">Complete Linkage</option>
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79 <option value="single">Single Linkage</option>
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80 <option value="ward" selected="true">Ward</option>
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81 <option value="mcquitty">Mcquitty</option>
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82 <option value="median">Median</option>
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83 <option value="centroid">Centroid</option>
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84 </param>
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85 </when>
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86 <when value="Original">
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87 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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88 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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89 </when>
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90 <when value="Random">
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91 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
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92 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
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93 </when>
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94 </conditional>
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95 <repeat name="operations" title="Covariate Bars">
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96 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">
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97 <sanitizer invalid_char="_">
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98 <valid initial="none">
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99 <add preset="string.letters"/>
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100 <add preset="string.digits"/>
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101 </valid>
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102 <mapping initial="none">
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103 </mapping>
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104 </sanitizer>
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105 </param>
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106 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>
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107 <param name="cat" type="select" label="Axis Covariate Type">
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108 <option value="row_categorical" >Row Categorical</option>
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109 <option value="row_continuous" >Row Continuous</option>
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110 <option value="column_categorical" >Column Categorical</option>
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111 <option value="column_continuous" >Column Continuous</option>
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112 </param>
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113 </repeat>
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114 </inputs>
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115 <outputs>
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116 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
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117 </outputs>
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118 <tests>
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119 <test>
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120 <param name="inputmatrix" value="400x400.txt" />
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121 <param name="hmname" value="testRun" />
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122 <param name="$hmdesc" value="validateTool" />
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123 <param name="summarymethod" value="Average" />
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124 <param name="rowOrderMethod" value="Hierarchical" />
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125 <param name="rowDistanceMeasure" value="Manhattan" />
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126 <param name="rowAgglomerationMethod" value="Ward" />
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127 <param name="columnOrderMethod" value="Hierarchical" />
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128 <param name="columnDistanceMeasure" value="Manhattan" />
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129 <param name="columnAgglomerationMethod" value="Ward" />
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130 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
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132 </test>
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133 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
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134 </tests>
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135 </tool>