|
13
|
1 <?xml version="1.0" encoding="UTF-8" ?>
|
|
32
|
2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.0.5">
|
|
13
|
3 <description>Create Clustered Heat Maps</description>
|
|
32
|
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'-->
|
|
|
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'
|
|
13
|
6 #for $op in $operations
|
|
|
7 ${op.class_name}
|
|
|
8 ${op.repeatinput.file_name}
|
|
|
9 ${op.cat}
|
|
|
10 #end for
|
|
|
11 '$output'
|
|
|
12 </command>
|
|
|
13 <stdio>
|
|
|
14 <exit_code range="1:" level="fatal" />
|
|
|
15 </stdio>
|
|
|
16 <inputs>
|
|
32
|
17 <param name="inputmatrix" type="data" format="Tabular" label="Input Matrix" />
|
|
|
18 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>
|
|
13
|
19 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>
|
|
|
20 <param name="summarymethod" type="select" label="Data Summarization Method">
|
|
32
|
21 <option value="average">Average</option>
|
|
|
22 <option value="sample">Sample</option>
|
|
|
23 <option value="mode">Mode</option>
|
|
13
|
24 </param>
|
|
|
25 <conditional name="d_rows">
|
|
|
26 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
|
|
|
27 <option value="Hierarchical">Hierarchical Clustering</option>
|
|
|
28 <option value="Original">Original Order</option>
|
|
|
29 <option value="Random">Random</option>
|
|
|
30 </param>
|
|
|
31 <when value="Hierarchical">
|
|
32
|
32 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
|
|
|
33 <option value="euclidean">Euclidean</option>
|
|
|
34 <option value="binary">Binary</option>
|
|
|
35 <option value="manhattan">Manhattan</option>
|
|
|
36 <option value="maximum">Maximum</option>
|
|
|
37 <option value="canberra">Canberra</option>
|
|
|
38 <option value="minkowski">Minkowski</option>
|
|
|
39 <option value="correlation">Correlation</option>
|
|
|
40 </param>
|
|
|
41 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
|
|
|
42 <option value="average">Average Linkage</option>
|
|
|
43 <option value="complete">Complete Linkage</option>
|
|
|
44 <option value="single">Single Linkage</option>
|
|
|
45 <option value="ward" selected="true">Ward</option>
|
|
|
46 <option value="mcquitty">Mcquitty</option>
|
|
|
47 <option value="median">Median</option>
|
|
|
48 <option value="centroid">Centroid</option>
|
|
|
49 </param>
|
|
13
|
50 </when>
|
|
|
51 <when value="Original">
|
|
32
|
52 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
|
|
|
53 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
|
|
13
|
54 </when>
|
|
|
55 <when value="Random">
|
|
32
|
56 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
|
|
|
57 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
|
|
13
|
58 </when>
|
|
|
59 </conditional>
|
|
|
60 <conditional name="d_cols">
|
|
|
61 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
|
|
|
62 <option value="Hierarchical">Hierarchical Clustering</option>
|
|
|
63 <option value="Original">Original Order</option>
|
|
|
64 <option value="Random">Random</option>
|
|
|
65 </param>
|
|
|
66 <when value="Hierarchical">
|
|
32
|
67 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
|
|
|
68 <option value="euclidean">Euclidean</option>
|
|
|
69 <option value="binary">Binary</option>
|
|
|
70 <option value="manhattan">Manhattan</option>
|
|
|
71 <option value="maximum">Maximum</option>
|
|
|
72 <option value="canberra">Canberra</option>
|
|
|
73 <option value="minkowski">Minkowski</option>
|
|
|
74 <option value="correlation">Correlation</option>
|
|
|
75 </param>
|
|
|
76 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
|
|
|
77 <option value="average">Average Linkage</option>
|
|
|
78 <option value="complete">Complete Linkage</option>
|
|
|
79 <option value="single">Single Linkage</option>
|
|
|
80 <option value="ward" selected="true">Ward</option>
|
|
|
81 <option value="mcquitty">Mcquitty</option>
|
|
|
82 <option value="median">Median</option>
|
|
|
83 <option value="centroid">Centroid</option>
|
|
|
84 </param>
|
|
13
|
85 </when>
|
|
|
86 <when value="Original">
|
|
32
|
87 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
|
|
|
88 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
|
|
13
|
89 </when>
|
|
|
90 <when value="Random">
|
|
32
|
91 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
|
|
|
92 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
|
|
13
|
93 </when>
|
|
|
94 </conditional>
|
|
|
95 <repeat name="operations" title="Covariate Bars">
|
|
|
96 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">
|
|
|
97 <sanitizer invalid_char="_">
|
|
|
98 <valid initial="none">
|
|
|
99 <add preset="string.letters"/>
|
|
|
100 <add preset="string.digits"/>
|
|
|
101 </valid>
|
|
|
102 <mapping initial="none">
|
|
|
103 </mapping>
|
|
|
104 </sanitizer>
|
|
|
105 </param>
|
|
|
106 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>
|
|
|
107 <param name="cat" type="select" label="Axis Covariate Type">
|
|
32
|
108 <option value="row_categorical" >Row Categorical</option>
|
|
|
109 <option value="row_continuous" >Row Continuous</option>
|
|
|
110 <option value="column_categorical" >Column Categorical</option>
|
|
|
111 <option value="column_continuous" >Column Continuous</option>
|
|
13
|
112 </param>
|
|
|
113 </repeat>
|
|
|
114 </inputs>
|
|
|
115 <outputs>
|
|
32
|
116 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
|
|
13
|
117 </outputs>
|
|
|
118 <tests>
|
|
|
119 <test>
|
|
|
120 <param name="inputmatrix" value="400x400.txt" />
|
|
|
121 <param name="hmname" value="testRun" />
|
|
|
122 <param name="$hmdesc" value="validateTool" />
|
|
32
|
123 <param name="summarymethod" value="Average" />
|
|
13
|
124 <param name="rowOrderMethod" value="Hierarchical" />
|
|
32
|
125 <param name="rowDistanceMeasure" value="Manhattan" />
|
|
|
126 <param name="rowAgglomerationMethod" value="Ward" />
|
|
13
|
127 <param name="columnOrderMethod" value="Hierarchical" />
|
|
32
|
128 <param name="columnDistanceMeasure" value="Manhattan" />
|
|
|
129 <param name="columnAgglomerationMethod" value="Ward" />
|
|
13
|
130 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
|
|
|
131
|
|
|
132 </test>
|
|
|
133 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
|
|
|
134 </tests>
|
|
|
135 </tool>
|
