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comparison mda_advanced_heatmap_gen.xml @ 0:8893ea2915cc draft

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Initial Version of Advanced Heat Map Tool
author insilico-bob
date Tue, 08 Aug 2017 14:01:05 -0400
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children 603f99d9e776
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-1:000000000000 0:8893ea2915cc
1 <?xml version="1.0" encoding="UTF-8" ?>
2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.0.5">
3 <description> Create Clustered Heat Maps</description>
4 <!-- command interpreter="python" detect_errors="aggressive">$__tool_directory__/mad_advanced_heatmap_gen.py 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType -->
5 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.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__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType
6
7 "
8 #for $attr in $hm_attribute
9 ${attr.attrbute_key}:${attr.attrbute_value};
10 #end for
11 "
12
13 #for $op in $operations
14 ${op.class_name}
15 ${op.repeatinput.file_name}
16 ${op.cat}
17 #end for
18 '$output'
19 </command>
20 <stdio>
21 <exit_code range="1:" level="fatal" />
22 </stdio>
23 <inputs>
24 <param name="inputmatrix" type="data" format="Tabular" label="Input Matrix" />
25 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>
26 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>
27 <param name="summarymethod" type="select" label="Data Summarization Method">
28 <option value="average">Average</option>
29 <option value="sample">Sample</option>
30 <option value="mode">Mode</option>
31 </param>
32 <conditional name="d_rows">
33 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
34 <option value="Hierarchical">Hierarchical Clustering</option>
35 <option value="Original">Original Order</option>
36 <option value="Random">Random</option>
37 </param>
38 <when value="Hierarchical">
39 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
40 <option value="euclidean">Euclidean</option>
41 <option value="binary">Binary</option>
42 <option value="manhattan">Manhattan</option>
43 <option value="maximum">Maximum</option>
44 <option value="canberra">Canberra</option>
45 <option value="minkowski">Minkowski</option>
46 <option value="correlation">Correlation</option>
47 </param>
48 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
49 <option value="average">Average Linkage</option>
50 <option value="complete">Complete Linkage</option>
51 <option value="single">Single Linkage</option>
52 <option value="ward" selected="true">Ward</option>
53 <option value="mcquitty">Mcquitty</option>
54 <option value="median">Median</option>
55 <option value="centroid">Centroid</option>
56 </param>
57 <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" >
58 <option value="0" selected="true" >None</option>
59 <option value="2" >2</option>
60 <option value="3" >3</option>
61 <option value="4" >4</option>
62 <option value="5" >5</option>
63 <option value="6" >6</option>
64 <option value="7" >7</option>
65 <option value="8" >8</option>
66 <option value="9" >9</option>
67 <option value="10" >10</option>
68 </param>
69 </when>
70 <when value="Original">
71 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
72 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
73 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
74 </when>
75 <when value="Random">
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 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
79 </when>
80 </conditional>
81 <param name="rowDataType" type="select" label="Linkouts to row data type info" >
82 <option value="labels" selected="true" >None</option>
83 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
84 <option value="bio.cbioportal.sampleid" >cBioPortal sample Id</option>
85 <option value="bio.gene.entrez" >Gene Entrez Id</option>
86 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
87 <option value="bio.go" >Gene Ontology (GO) Id</option>
88 <option value="bio.geo.acc" >GEO Accession Id</option>
89 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
90 <option value="bio.mirna" >miRNA Id</option>
91 <option value="bio.pubmed.search" >Pubmed Search Term</option>
92 <option value="scholar" >Scholarly term</option>
93 <option value="bio.protein.uniprotid" >UniProt Id</option>
94 </param>
95 <conditional name="d_cols">
96 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
97 <option value="Hierarchical">Hierarchical Clustering</option>
98 <option value="Original">Original Order</option>
99 <option value="Random">Random</option>
100 </param>
101 <when value="Hierarchical">
102 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="Euclidean, Binary, Manhattan, Maximum, Canberra, Minkowski, or Correlation">
103 <option value="euclidean">Euclidean</option>
104 <option value="binary">Binary</option>
105 <option value="manhattan">Manhattan</option>
106 <option value="maximum">Maximum</option>
107 <option value="canberra">Canberra</option>
108 <option value="minkowski">Minkowski</option>
109 <option value="correlation">Correlation</option>
110 </param>
111 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: Average Linkage, Complete Linkage, Single Linkage, 'Ward', 'Mcquitty', 'Median', or 'Centroid'.">
112 <option value="average">Average Linkage</option>
113 <option value="complete">Complete Linkage</option>
114 <option value="single">Single Linkage</option>
115 <option value="ward" selected="true">Ward</option>
116 <option value="mcquitty">Mcquitty</option>
117 <option value="median">Median</option>
118 <option value="centroid">Centroid</option>
119 </param>
120 <param name="colDendroCut" type="select" label="Create column categorical covariate bar based on number of top-level dendrogram clusters" >
121 <option value="0" selected="true" >None</option>
122 <option value="2" >2</option>
123 <option value="3" >3</option>
124 <option value="4" >4</option>
125 <option value="5" >5</option>
126 <option value="6" >6</option>
127 <option value="7" >7</option>
128 <option value="8" >8</option>
129 <option value="9" >9</option>
130 <option value="10" >10</option>
131 </param>
132 </when>
133 <when value="Original">
134 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
135 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
136 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
137 </when>
138 <when value="Random">
139 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
140 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
141 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
142 </when>
143 </conditional>
144 <param name="colDataType" type="select" label="Linkouts to column data type info" >
145 <option value="labels" selected="true" >None</option>
146 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
147 <option value="bio.cbioportal.sampleid" >cBioPortal sample Id</option>
148 <option value="bio.gene.entrez" >Gene Entrez Id</option>
149 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
150 <option value="bio.go" >Gene Ontology (GO) Id</option>
151 <option value="bio.geo.acc" >GEO Accession Id</option>
152 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
153 <option value="bio.mirna" >miRNA Id</option>
154 <option value="bio.pubmed.search" >Pubmed Search Term</option>
155 <option value="scholar" >Scholarly term</option>
156 <option value="bio.protein.uniprotid" >UniProt Id</option>
157 </param>
158 <repeat name="operations" title="Covariate Bars">
159 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">
160 <sanitizer invalid_char="_">
161 <valid initial="none">
162 <add preset="string.letters"/>
163 <add preset="string.digits"/>
164 </valid>
165 <mapping initial="none">
166 </mapping>
167 </sanitizer>
168 </param>
169 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>
170 <param name="cat" type="select" label="Axis Covariate Type">
171 <option value="row_categorical" >Row Categorical</option>
172 <option value="row_continuous" >Row Continuous</option>
173 <option value="column_categorical" >Column Categorical</option>
174 <option value="column_continuous" >Column Continuous</option>
175 </param>
176 </repeat>
177 <repeat name="hm_attribute" title="Heat Map Attributes">
178 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attributes json pair-- key ">
179 <sanitizer invalid_char="_">
180 <valid initial="">
181 <add preset="string.letters"/>
182 <add preset="string.digits"/>
183 </valid>
184 <mapping initial="">
185 </mapping>
186 </sanitizer>
187 </param>
188 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes json pairs -- value ">
189 <sanitizer invalid_char="_">
190 <valid initial="">
191 <add preset="string.letters"/>
192 <add preset="string.digits"/>
193 </valid>
194 <mapping initial="">
195 </mapping>
196 </sanitizer>
197 </param>
198 </repeat>
199 </inputs>
200 <outputs>
201 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
202 </outputs>
203 <tests>
204 <test>
205 <param name="inputmatrix" value="400x400.txt" />
206 <param name="hmname" value="testRun" />
207 <param name="$hmdesc" value="validateTool" />
208 <param name="summarymethod" value="Average" />
209 <param name="rowOrderMethod" value="Hierarchical" />
210 <param name="rowDistanceMeasure" value="Manhattan" />
211 <param name="rowAgglomerationMethod" value="Ward" />
212 <param name="columnOrderMethod" value="Hierarchical" />
213 <param name="columnDistanceMeasure" value="Manhattan" />
214 <param name="columnAgglomerationMethod" value="Ward" />
215 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
216
217 </test>
218 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
219 </tests>
220 </tool>