Mercurial > repos > md-anderson-bioinformatics > heat_map_creation

comparison mda_heatmap_gen.xml @ 40:8f8ab332a050 draft

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author insilico-bob
date Thu, 20 Jun 2019 11:39:46 -0400
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39:436f03b71cf6 40:8f8ab332a050
1 <?xml version="1.0" encoding="UTF-8" ?>
2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.3">
3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <requirement type="package" version="8.0.144">openjdk</requirement>
6 </requirements>
7 <description>Create Clustered Heat Maps</description>
8 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc"
9 "matrix_files|path|$inputmatrix|name|datalayer|summary_method|$summarymethod"
10 "row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|0|data_type|labels"
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"
12 #for $op in $operations
13 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cat}'
14 #end for
15 'output_location|$output'
16 </command>
17 <stdio>
18 <exit_code range="1:" level="fatal" />
19 </stdio>
20 <inputs>
21 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data." />
22 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
23 <sanitizer>
24 <valid>
25 <add preset="string.printable"/>
26 <remove value="&quot;"/>
27 <remove value="&apos;"/>
28 <remove value=" "/>
29 </valid>
30 </sanitizer>
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."/>
32 <sanitizer>
33 <valid>
34 <add preset="string.printable"/>
35 <add value="string.letters"/>
36 <add value="string.digits"/>
37 <add value="-"/>
38 <add value="_"/>
39 <remove value="&quot;"/>
40 <remove value="&apos;"/>
41 <remove value=" "/>
42 </valid>
43 </sanitizer>
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.">
45 <option value="average">Average</option>
46 <option value="sample">Sample</option>
47 <option value="mode">Mode</option>
48 </param>
49 <conditional name="d_rows">
50 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is.">
51 <option value="Hierarchical">Hierarchical Clustering</option>
52 <option value="Original">Original Order</option>
53 <option value="Random">Random</option>
54 </param>
55 <when value="Hierarchical">
56 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows">
57 <option value="euclidean">Euclidean</option>
58 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
59 <option value="manhattan">Manhattan</option>
60 <option value="maximum">Maximum</option>
61 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
62 <option value="minkowski">Minkowski</option>
63 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
64 </param>
65 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
66 <option value="average">Average Linkage</option>
67 <option value="complete">Complete Linkage</option>
68 <option value="single">Single Linkage</option>
69 <option value="ward" selected="true">Ward</option>
70 <option value="mcquitty">Mcquitty</option>
71 <!-- <option value="median">Median</option> ** breaks dendrogram
72 <option value="centroid">Centroid</option> ** breaks dendrogram -->
73 </param>
74 </when>
75 <when value="Original">
76 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
77 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
78 </when>
79 <when value="Random">
80 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
81 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
82 </when>
83 </conditional>
84 <conditional name="d_cols">
85 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is.">
86 <option value="Hierarchical">Hierarchical Clustering</option>
87 <option value="Original">Original Order</option>
88 <option value="Random">Random</option>
89 </param>
90 <when value="Hierarchical">
91 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns">
92 <option value="euclidean">Euclidean</option>
93 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
94 <option value="manhattan">Manhattan</option>
95 <option value="maximum">Maximum</option>
96 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
97 <option value="minkowski">Minkowski</option>
98 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
99 </param>
100 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
101 <option value="average">Average Linkage</option>
102 <option value="complete">Complete Linkage</option>
103 <option value="single">Single Linkage</option>
104 <option value="ward" selected="true">Ward</option>
105 <option value="mcquitty">Mcquitty</option>
106 <!-- <option value="median">Median</option> ** breaks dendrogram
107 <option value="centroid">Centroid</option> ** breaks dendrogram -->
108 </param>
109 </when>
110 <when value="Original">
111 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
112 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
113 </when>
114 <when value="Random">
115 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
116 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
117 </when>
118 </conditional>
119 <repeat name="operations" title="Covariate Bars">
120 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
121 <sanitizer>
122 <valid>
123 <add preset="string.printable"/>
124 <remove value="&quot;"/>
125 <remove value="&apos;"/>
126 <remove value=" "/>
127 </valid>
128 </sanitizer>
129 </param>
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."/>
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.">
132 <option value="row_discrete" >Row Categorical</option>
133 <option value="row_continuous" >Row Continuous</option>
134 <option value="column_discrete" >Column Categorical</option>
135 <option value="column_continuous" >Column Continuous</option>
136 </param>
137 </repeat>
138 </inputs>
139 <outputs>
140 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
141 </outputs>
142 <tests>
143 <test>
144 <param name="inputmatrix" value="400x400.txt" />
145 <param name="hmname" value="testRun" />
146 <param name="$hmdesc" value="validateTool" />
147 <param name="summarymethod" value="Average" />
148 <param name="rowOrderMethod" value="Hierarchical" />
149 <param name="rowDistanceMeasure" value="Manhattan" />
150 <param name="rowAgglomerationMethod" value="Ward" />
151 <param name="columnOrderMethod" value="Hierarchical" />
152 <param name="columnDistanceMeasure" value="Manhattan" />
153 <param name="columnAgglomerationMethod" value="Ward" />
154 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
155
156 </test>
157 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
158 </tests>
159 </tool>