|
1
|
1 <?xml version="1.0" encoding="UTF-8" ?>
|
|
|
2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="6.0.2">
|
|
|
3 <description>Create Clustered Heat Maps</description>
|
|
|
4 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh '$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 #for $op in $operations
|
|
|
6 ${op.class_name}
|
|
|
7 ${op.repeatinput.file_name}
|
|
|
8 ${op.cat}
|
|
|
9 #end for
|
|
|
10 '$output'
|
|
|
11 </command>
|
|
|
12 <stdio>
|
|
|
13 <exit_code range="1:" level="fatal" />
|
|
|
14 </stdio>
|
|
|
15 <inputs>
|
|
|
16 <param name="inputmatrix" type="data" label="Input Matrix" />
|
|
|
17 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="User Defined Heat Map Name"/>
|
|
|
18 <param name="hmdesc" size="100" optional="true" type="text" value="Heat_Map_description" label="User Defined Heat Map Description"/>
|
|
|
19 <param name="summarymethod" type="select" label="Data Summarization Method">
|
|
|
20 <option value="average">average</option>
|
|
|
21 <option value="sample">sample</option>
|
|
|
22 <option value="mode">mode</option>
|
|
|
23 </param>
|
|
|
24 <conditional name="d_rows">
|
|
|
25 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
|
|
|
26 <option value="Hierarchical">Hierarchical Clustering</option>
|
|
|
27 <option value="Original">Original Order</option>
|
|
|
28 <option value="Random">Random</option>
|
|
|
29 </param>
|
|
|
30 <when value="Hierarchical">
|
|
|
31 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation">
|
|
|
32 <option value="euclidean">Euclidean</option>
|
|
|
33 <option value="binary">Binary</option>
|
|
|
34 <option value="manhattan">Manhattan</option>
|
|
|
35 <option value="maximum">Maximum</option>
|
|
|
36 <option value="canberra">Canberra</option>
|
|
|
37 <option value="minkowski">Minkowski</option>
|
|
|
38 <option value="correlation">Correlation</option>
|
|
|
39 </param>
|
|
|
40 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'.">
|
|
|
41 <option value="average">Average Linkage</option>
|
|
|
42 <option value="complete">Complete Linkage</option>
|
|
|
43 <option value="single">Single Linkage</option>
|
|
|
44 <option value="ward" selected="true">Ward</option>
|
|
|
45 <option value="mcquitty">Mcquitty</option>
|
|
|
46 <option value="median">Median</option>
|
|
|
47 <option value="centroid">Centroid</option>
|
|
|
48 </param>
|
|
|
49 <param name="rowDendroCut" type="select" label="Create row categorical covariate bar based on number of top-level dendrogram clusters" >
|
|
|
50 <option value="0" selected="true" >None</option>
|
|
|
51 <option value="2" >2</option>
|
|
|
52 <option value="3" >3</option>
|
|
|
53 <option value="4" >4</option>
|
|
|
54 <option value="5" >5</option>
|
|
|
55 <option value="6" >6</option>
|
|
|
56 <option value="7" >7</option>
|
|
|
57 <option value="8" >8</option>
|
|
|
58 <option value="9" >9</option>
|
|
|
59 <option value="10" >10</option>
|
|
|
60 </param>
|
|
|
61 </when>
|
|
|
62 <when value="Original">
|
|
|
63 <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/>
|
|
|
64 <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/>
|
|
|
65 <param name="rowDendroCut" size="0" type="text" value="0"/>
|
|
|
66 </when>
|
|
|
67 <when value="Random">
|
|
|
68 <param name="rowDistanceMeasure" type="text" size="0" value="n/a"/>
|
|
|
69 <param name="rowAgglomerationMethod" type="text" size="0" value="n/a"/>
|
|
|
70 <param name="rowDendroCut" type="text" size="0" value="0"/>
|
|
|
71 </when>
|
|
|
72 </conditional>
|
|
|
73 <param name="rowDataType" type="select" label="Linkouts to row data type info" >
|
|
|
74 <option value="labels" selected="true" >None</option>
|
|
|
75 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
|
|
|
76 <option value="bio.feature.agilent" >Agilent Id</option>
|
|
|
77 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
|
|
|
78 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
|
|
|
79 <option value="bio.gene.entrez" >Gene Entrez Id</option>
|
|
|
80 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
|
|
|
81 <option value="bio.go" >Gene Ontology (GO) Id</option>
|
|
|
82 <option value="bio.geo.acc" >GEO Accession Id</option>
|
|
|
83 <option value="bio.probe.illumina" >Illumina Probe Id</option>
|
|
|
84 <option value="bio.probe.infinium" >Infinium Probe Id</option>
|
|
|
85 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
|
|
|
86 <option value="bio.mirna" >miRNA Id</option>
|
|
|
87 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
|
|
|
88 <option value="bio.pubmed" >Pubmed Id</option>
|
|
|
89 <option value="bio.pubmed.search" >Pubmed Search Term</option>
|
|
|
90 <option value="scholar" >Scholarly term</option>
|
|
|
91 <option value="bio.gene.unigene" >Unigene CID</option>
|
|
|
92 <option value="bio.protein.uniprot" >UniProt Id</option>
|
|
|
93 </param>
|
|
|
94 <conditional name="d_cols">
|
|
|
95 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Choices -- Hierarchical Clustering, Original Order, Random">
|
|
|
96 <option value="Hierarchical">Hierarchical Clustering</option>
|
|
|
97 <option value="Original">Original Order</option>
|
|
|
98 <option value="Random">Random</option>
|
|
|
99 </param>
|
|
|
100 <when value="Hierarchical">
|
|
|
101 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="euclidean, binary, manhattan, maximum, canberra, minkowski, or correlation">
|
|
|
102 <option value="euclidean">Euclidean</option>
|
|
|
103 <option value="binary">Binary</option>
|
|
|
104 <option value="manhattan">Manhattan</option>
|
|
|
105 <option value="maximum">Maximum</option>
|
|
|
106 <option value="canberra">Canberra</option>
|
|
|
107 <option value="minkowski">Minkowski</option>
|
|
|
108 <option value="correlation">Correlation</option>
|
|
|
109 </param>
|
|
|
110 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="Choices: 'average' for Average Linkage, 'complete' for Complete Linkage, 'single' for Single Linkage, 'ward', 'mcquitty', 'median', or 'centroid'.">
|
|
|
111 <option value="average">Average Linkage</option>
|
|
|
112 <option value="complete">Complete Linkage</option>
|
|
|
113 <option value="single">Single Linkage</option>
|
|
|
114 <option value="ward" selected="true">Ward</option>
|
|
|
115 <option value="mcquitty">Mcquitty</option>
|
|
|
116 <option value="median">Median</option>
|
|
|
117 <option value="centroid">Centroid</option>
|
|
|
118 </param>
|
|
|
119 <param name="colDendroCut" type="select" label="Create column categorical covariate bar based on number of top-level dendrogram clusters" >
|
|
|
120 <option value="0" selected="true" >None</option>
|
|
|
121 <option value="2" >2</option>
|
|
|
122 <option value="3" >3</option>
|
|
|
123 <option value="4" >4</option>
|
|
|
124 <option value="5" >5</option>
|
|
|
125 <option value="6" >6</option>
|
|
|
126 <option value="7" >7</option>
|
|
|
127 <option value="8" >8</option>
|
|
|
128 <option value="9" >9</option>
|
|
|
129 <option value="10" >10</option>
|
|
|
130 </param>
|
|
|
131 </when>
|
|
|
132 <when value="Original">
|
|
|
133 <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/>
|
|
|
134 <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/>
|
|
|
135 <param name="colDendroCut" type="text" size="0" value="0"/>
|
|
|
136 </when>
|
|
|
137 <when value="Random">
|
|
|
138 <param name="columnDistanceMeasure" type="text" size="0" value="n/a"/>
|
|
|
139 <param name="columnAgglomerationMethod" type="text" size="0" value="n/a"/>
|
|
|
140 <param name="colDendroCut" type="text" size="0" value="0"/>
|
|
|
141 </when>
|
|
|
142 </conditional>
|
|
|
143 <param name="colDataType" type="select" label="Linkouts to column data type info" >
|
|
|
144 <option value="labels" selected="true" >None</option>
|
|
|
145 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
|
|
|
146 <option value="bio.feature.agilent" >Agilent Id</option>
|
|
|
147 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
|
|
|
148 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
|
|
|
149 <option value="bio.gene.entrez" >Gene Entrez Id</option>
|
|
|
150 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
|
|
|
151 <option value="bio.go" >Gene Ontology (GO) Id</option>
|
|
|
152 <option value="bio.geo.acc" >GEO Accession Id</option>
|
|
|
153 <option value="bio.probe.illumina" >Illumina Probe Id</option>
|
|
|
154 <option value="bio.probe.infinium" >Infinium Probe Id</option>
|
|
|
155 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
|
|
|
156 <option value="bio.mirna" >miRNA Id</option>
|
|
|
157 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
|
|
|
158 <option value="bio.pubmed" >Pubmed Id</option>
|
|
|
159 <option value="bio.pubmed.search" >Pubmed Search Term</option>
|
|
|
160 <option value="scholar" >Scholarly term</option>
|
|
|
161 <option value="bio.gene.unigene" >Unigene CId</option>
|
|
|
162 <option value="bio.protein.uniprot" >UniProt Id</option>
|
|
|
163 </param>
|
|
|
164 <repeat name="operations" title="Covariate Bars">
|
|
|
165 <param name="class_name" size="20" type="text" value="" label="Axis Covariate Name">
|
|
|
166 <sanitizer invalid_char="_">
|
|
|
167 <valid initial="none">
|
|
|
168 <add preset="string.letters"/>
|
|
|
169 <add preset="string.digits"/>
|
|
|
170 </valid>
|
|
|
171 <mapping initial="none">
|
|
|
172 </mapping>
|
|
|
173 </sanitizer>
|
|
|
174 </param>
|
|
|
175 <param name="repeatinput" type="data" format="text" label="Axis Covariate File"/>
|
|
|
176 <param name="cat" type="select" label="Axis Covariate Type">
|
|
|
177 <option value="row_categorical" >row categorical</option>
|
|
|
178 <option value="row_continuous" >row continuous</option>
|
|
|
179 <option value="column_categorical" >column categorical</option>
|
|
|
180 <option value="column_continuous" >column continuous</option>
|
|
|
181 </param>
|
|
|
182 </repeat>
|
|
|
183 </inputs>
|
|
|
184 <outputs>
|
|
|
185 <data name="output" label='${hmname}' format="ngchm"/>
|
|
|
186 </outputs>
|
|
|
187 <tests>
|
|
|
188 <test>
|
|
|
189 <param name="inputmatrix" value="400x400.txt" />
|
|
|
190 <param name="hmname" value="testRun" />
|
|
|
191 <param name="$hmdesc" value="validateTool" />
|
|
|
192 <param name="summarymethod" value="average" />
|
|
|
193 <param name="rowOrderMethod" value="Hierarchical" />
|
|
|
194 <param name="rowDistanceMeasure" value="manhattan" />
|
|
|
195 <param name="rowAgglomerationMethod" value="ward" />
|
|
|
196 <param name="columnOrderMethod" value="Hierarchical" />
|
|
|
197 <param name="columnDistanceMeasure" value="manhattan" />
|
|
|
198 <param name="columnAgglomerationMethod" value="ward" />
|
|
|
199 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
|
|
|
200
|
|
|
201 </test>
|
|
|
202 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
|
|
|
203 </tests>
|
|
|
204 </tool>
|
