Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
annotate mda_advanced_heatmap_gen.xml @ 4:d747292c486f draft
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author | insilico-bob |
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date | Tue, 06 Nov 2018 16:30:12 -0500 |
parents | 9359e0a0d40b |
children | 15c71ed09efa |
rev | line source |
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1 | 1 <?xml version="1.0" encoding="UTF-8" ?> |
4 | 2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3"> |
2 | 3 <requirements> |
4 | 4 <requirement type="package" version="3.4.1">r-base</requirement> |
5 <requirement type="package" version="8.0.144">openjdk</requirement> | |
2 | 6 </requirements> |
7 <description> Create Clustered Heat Maps with Advanced Options</description> | |
4 | 8 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh 'advanced' 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__;$__tool_data_path__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' |
1 | 9 |
10 " | |
11 #for $attr in $hm_attribute | |
3
9359e0a0d40b
Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
insilico-bob
parents:
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diff
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12 '${attr.attrbute_key}':'${attr.attrbute_value}'; |
1 | 13 #end for |
14 " | |
15 | |
16 #for $op in $operations | |
3
9359e0a0d40b
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insilico-bob
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17 '${op.class_name}' |
9359e0a0d40b
Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
insilico-bob
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18 '${op.repeatinput.file_name}' |
9359e0a0d40b
Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
insilico-bob
parents:
2
diff
changeset
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19 '${op.cattype.cat}' |
9359e0a0d40b
Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
insilico-bob
parents:
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20 '${op.cattype.bartype}' |
1 | 21 #end for |
22 '$output' | |
23 </command> | |
24 <stdio> | |
25 <exit_code range="1:" level="fatal" /> | |
26 </stdio> | |
27 <inputs> | |
28 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/> | |
2 | 29 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> |
30 <sanitizer> | |
31 <valid> | |
32 <add preset="string.printable"/> | |
33 <remove value="""/> | |
34 <remove value="'"/> | |
35 <remove value=" "/> | |
36 </valid> | |
37 </sanitizer> | |
1 | 38 <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."/> |
2 | 39 <sanitizer> |
40 <valid> | |
41 <add preset="string.printable"/> | |
42 <remove value="""/> | |
43 <remove value="'"/> | |
44 <remove value=" "/> | |
45 </valid> | |
46 </sanitizer> | |
1 | 47 <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."> |
48 <option value="average">Average</option> | |
49 <option value="sample">Sample</option> | |
50 <option value="mode">Mode</option> | |
51 </param> | |
52 <conditional name="d_rows"> | |
53 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is."> | |
54 <option value="Hierarchical">Hierarchical Clustering</option> | |
55 <option value="Original">Original Order</option> | |
56 <option value="Random">Random</option> | |
57 </param> | |
58 <when value="Hierarchical"> | |
59 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows."> | |
60 <option value="euclidean">Euclidean</option> | |
61 <option value="binary">Binary</option> | |
62 <option value="manhattan">Manhattan</option> | |
63 <option value="maximum">Maximum</option> | |
64 <option value="canberra">Canberra</option> | |
65 <option value="minkowski">Minkowski</option> | |
66 <option value="correlation">Correlation</option> | |
67 </param> | |
68 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters."> | |
69 <option value="average">Average Linkage</option> | |
70 <option value="complete">Complete Linkage</option> | |
71 <option value="single">Single Linkage</option> | |
72 <option value="ward" selected="true">Ward</option> | |
73 <option value="mcquitty">Mcquitty</option> | |
74 <option value="median">Median</option> | |
75 <option value="centroid">Centroid</option> | |
76 </param> | |
77 <param name="rowDendroCut" type="select" label="Row Cluster Covariate Bar" help="To generate a row covariate bar based on clusters, select the number of clusters(classes) to use."> | |
78 <option value="0" selected="true" >None</option> | |
79 <option value="2" >2</option> | |
80 <option value="3" >3</option> | |
81 <option value="4" >4</option> | |
82 <option value="5" >5</option> | |
83 <option value="6" >6</option> | |
84 <option value="7" >7</option> | |
85 <option value="8" >8</option> | |
86 <option value="9" >9</option> | |
87 <option value="10" >10</option> | |
88 </param> | |
89 <conditional name="rcutrows"> | |
90 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
91 <option value="none">None</option> | |
92 <option value="treecuts">Cluster-Based Gaps</option> | |
93 <option value="positional">Fixed Gaps</option> | |
94 </param> | |
95 <when value="none"> | |
96 <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/> | |
97 </when> | |
98 <when value="treecuts"> | |
99 <param name="rowDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters." > | |
100 <option value="0t" selected="true" >None</option> | |
101 <option value="2t" >2</option> | |
102 <option value="3t" >3</option> | |
103 <option value="4t" >4</option> | |
104 <option value="5t" >5</option> | |
105 <option value="6t" >6</option> | |
106 <option value="7t" >7</option> | |
107 <option value="8t" >8</option> | |
108 <option value="9t" >9</option> | |
109 <option value="10t" >10</option> | |
110 </param> | |
111 </when> | |
112 <when value="positional"> | |
113 <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> | |
114 </when> | |
115 </conditional> | |
116 </when> | |
117 <when value="Original"> | |
118 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | |
119 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
120 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> | |
121 <conditional name="rcutrows"> | |
122 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
123 <option value="none">None</option> | |
124 <option value="positional">Fixed Gaps</option> | |
125 </param> | |
126 <when value="none"> | |
127 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
128 </when> | |
129 <when value="positional"> | |
130 <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> | |
131 </when> | |
132 </conditional> | |
133 </when> | |
134 <when value="Random"> | |
135 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | |
136 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
137 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> | |
138 <conditional name="rcutrows"> | |
139 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
140 <option value="none">None</option> | |
141 <option value="positional">Fixed Gaps</option> | |
142 </param> | |
143 <when value="none"> | |
144 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
145 </when> | |
146 <when value="positional"> | |
147 <param name="rowDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> | |
148 </when> | |
149 </conditional> | |
150 </when> | |
151 </conditional> | |
152 <param name="rowTopItems" size="100" type="text" value="None" label="Row Top Items" help="A few rows can be labeled in the full summary heat map. To do so provide a comma delimited list of row labels."/> | |
153 <param name="rowDataType" type="select" label="Row Label Type" help="Enable label driven link-outs by specifying the type of row labels."> | |
154 <option value="labels" selected="true" >None</option> | |
155 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option> | |
156 <option value="bio.feature.agilent" >Agilent Id</option> | |
157 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option> | |
158 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option> | |
159 <option value="bio.gene.entrez" >Gene Entrez Id</option> | |
160 <option value="bio.gene.hugo" >Gene HUGO symbol</option> | |
161 <option value="bio.go" >Gene Ontology (GO) Id</option> | |
162 <option value="bio.geo.acc" >GEO Accession Id</option> | |
163 <option value="bio.probe.illumina" >Illumina Probe Id</option> | |
164 <option value="bio.probe.infinium" >Infinium Probe Id</option> | |
165 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option> | |
166 <option value="bio.mirna" >miRNA Id</option> | |
167 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option> | |
168 <option value="bio.pubmed" >Pubmed Id</option> | |
169 <option value="bio.pubmed.search" >Pubmed Search Term</option> | |
170 <option value="scholar" >Scholarly term</option> | |
171 <option value="bio.gene.unigene" >Unigene CId</option> | |
172 <option value="bio.protein.uniprot" >UniProt Id</option> | |
173 </param> | |
174 <conditional name="d_cols"> | |
175 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is."> | |
176 <option value="Hierarchical">Hierarchical Clustering</option> | |
177 <option value="Original">Original Order</option> | |
178 <option value="Random">Random</option> | |
179 </param> | |
180 <when value="Hierarchical"> | |
181 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns."> | |
182 <option value="euclidean">Euclidean</option> | |
183 <option value="binary">Binary</option> | |
184 <option value="manhattan">Manhattan</option> | |
185 <option value="maximum">Maximum</option> | |
186 <option value="canberra">Canberra</option> | |
187 <option value="minkowski">Minkowski</option> | |
188 <option value="correlation">Correlation</option> | |
189 </param> | |
190 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters."> | |
191 <option value="average">Average Linkage</option> | |
192 <option value="complete">Complete Linkage</option> | |
193 <option value="single">Single Linkage</option> | |
194 <option value="ward" selected="true">Ward</option> | |
195 <option value="mcquitty">Mcquitty</option> | |
196 <option value="median">Median</option> | |
197 <option value="centroid">Centroid</option> | |
198 </param> | |
199 <param name="colDendroCut" type="select" label="Column Cluster Covariate Bar" help="To generate a column covariate bar based on clusters, select the number of clusters(classes) to use."> | |
200 <option value="0" selected="true" >None</option> | |
201 <option value="2" >2</option> | |
202 <option value="3" >3</option> | |
203 <option value="4" >4</option> | |
204 <option value="5" >5</option> | |
205 <option value="6" >6</option> | |
206 <option value="7" >7</option> | |
207 <option value="8" >8</option> | |
208 <option value="9" >9</option> | |
209 <option value="10" >10</option> | |
210 </param> | |
211 <conditional name="ccutrows"> | |
212 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
213 <option value="none">None</option> | |
214 <option value="treecuts">Cluster-Based Gaps</option> | |
215 <option value="positional">Fixed Gaps</option> | |
216 </param> | |
217 <when value="none"> | |
218 <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/> | |
219 </when> | |
220 <when value="treecuts"> | |
221 <param name="colDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters."> | |
222 <option value="0t" selected="true" >None</option> | |
223 <option value="2t" >2</option> | |
224 <option value="3t" >3</option> | |
225 <option value="4t" >4</option> | |
226 <option value="5t" >5</option> | |
227 <option value="6t" >6</option> | |
228 <option value="7t" >7</option> | |
229 <option value="8t" >8</option> | |
230 <option value="9t" >9</option> | |
231 <option value="10t" >10</option> | |
232 </param> | |
233 </when> | |
234 <when value="positional"> | |
235 <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> | |
236 </when> | |
237 </conditional> | |
238 </when> | |
239 <when value="Original"> | |
240 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | |
241 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
242 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> | |
243 <conditional name="ccutrows"> | |
244 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
245 <option value="none">None</option> | |
246 <option value="positional">Fixed Gaps</option> | |
247 </param> | |
248 <when value="none"> | |
249 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
250 </when> | |
251 <when value="positional"> | |
252 <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> | |
253 </when> | |
254 </conditional> | |
255 </when> | |
256 <when value="Random"> | |
257 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> | |
258 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> | |
259 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> | |
260 <conditional name="ccutrows"> | |
261 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method."> | |
262 <option value="none">None</option> | |
263 <option value="positional">Fixed Gaps</option> | |
264 </param> | |
265 <when value="none"> | |
266 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/> | |
267 </when> | |
268 <when value="positional"> | |
269 <param name="colDendroTreeCut" type="text" size="100" value="None" label="Fixed Gap Location(s)" help="Enter a comma delimited list of row numbers where gaps should be created."/> | |
270 </when> | |
271 </conditional> | |
272 </when> | |
273 </conditional> | |
274 <param name="colTopItems" size="100" type="text" value="None" label="Column Top Items" help="A few columns can be labeled in the full summary heat map. To do so provide a comma delimited list of column labels."/> | |
275 <param name="colDataType" type="select" label="Column Label Type" help="Enable label driven link-outs by specifying the type of column labels."> | |
276 <option value="labels" selected="true" >None</option> | |
277 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option> | |
278 <option value="bio.feature.agilent" >Agilent Id</option> | |
279 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option> | |
280 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option> | |
281 <option value="bio.gene.entrez" >Gene Entrez Id</option> | |
282 <option value="bio.gene.hugo" >Gene HUGO symbol</option> | |
283 <option value="bio.go" >Gene Ontology (GO) Id</option> | |
284 <option value="bio.geo.acc" >GEO Accession Id</option> | |
285 <option value="bio.probe.illumina" >Illumina Probe Id</option> | |
286 <option value="bio.probe.infinium" >Infinium Probe Id</option> | |
287 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option> | |
288 <option value="bio.mirna" >miRNA Id</option> | |
289 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option> | |
290 <option value="bio.pubmed" >Pubmed Id</option> | |
291 <option value="bio.pubmed.search" >Pubmed Search Term</option> | |
292 <option value="scholar" >Scholarly term</option> | |
293 <option value="bio.gene.unigene" >Unigene CId</option> | |
294 <option value="bio.protein.uniprot" >UniProt Id</option> | |
295 </param> | |
296 <repeat name="operations" title="Covariate Bars"> | |
2 | 297 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label."> |
298 <sanitizer> | |
299 <valid> | |
300 <add preset="string.printable"/> | |
301 <remove value="""/> | |
302 <remove value="'"/> | |
303 <remove value=" "/> | |
1 | 304 </valid> |
305 </sanitizer> | |
306 </param> | |
2 | 307 <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."/> |
1 | 308 <conditional name="cattype"> |
309 <param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> | |
310 <option value="row_categorical" >Row Categorical</option> | |
311 <option value="row_continuous" >Row Continuous</option> | |
312 <option value="column_categorical" >Column Categorical</option> | |
313 <option value="column_continuous" >Column Continuous</option> | |
314 </param> | |
315 <when value="row_continuous"> | |
316 <param name="bartype" type="select" label="Display Type"> | |
317 <option value="color_plot" >Standard</option> | |
318 <option value="bar_plot" >Bar Plot</option> | |
319 <option value="scatter_plot" >Scatter Plot</option> | |
320 </param> | |
321 </when> | |
322 <when value="column_continuous"> | |
323 <param name="bartype" type="select" label="Display Type"> | |
324 <option value="color_plot" >Standard</option> | |
325 <option value="bar_plot" >Bar Plot</option> | |
326 <option value="scatter_plot" >Scatter Plot</option> | |
327 </param> | |
328 </when> | |
329 <when value="column_categorical"> | |
330 <param name="bartype" type="text" hidden="true" value="color_plot"/> | |
331 </when> | |
332 <when value="row_categorical"> | |
333 <param name="bartype" type="text" hidden="true" value="color_plot"/> | |
334 </when> | |
335 </conditional> | |
336 </repeat> | |
337 <repeat name="hm_attribute" title="Heat Map Attributes"> | |
338 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces)."> | |
339 <sanitizer invalid_char="_"> | |
340 <valid initial=""> | |
341 <add preset="string.letters"/> | |
342 <add preset="string.digits"/> | |
343 </valid> | |
344 <mapping initial=""> | |
345 </mapping> | |
346 </sanitizer> | |
347 </param> | |
348 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces)."> | |
349 <sanitizer invalid_char="_"> | |
350 <valid initial=""> | |
351 <add preset="string.letters"/> | |
352 <add preset="string.digits"/> | |
353 </valid> | |
354 <mapping initial=""> | |
355 </mapping> | |
356 </sanitizer> | |
357 </param> | |
358 </repeat> | |
359 </inputs> | |
360 <outputs> | |
361 <data name="output" label='Heat_Map_$hmname' format="ngchm"/> | |
362 </outputs> | |
363 <tests> | |
364 <test> | |
365 <param name="inputmatrix" value="400x400.txt" /> | |
366 <param name="hmname" value="testRun" /> | |
367 <param name="$hmdesc" value="validateTool" /> | |
368 <param name="summarymethod" value="Average" /> | |
369 <param name="rowOrderMethod" value="Hierarchical" /> | |
370 <param name="rowDistanceMeasure" value="Manhattan" /> | |
371 <param name="rowAgglomerationMethod" value="Ward" /> | |
372 <param name="columnOrderMethod" value="Hierarchical" /> | |
373 <param name="columnDistanceMeasure" value="Manhattan" /> | |
374 <param name="columnAgglomerationMethod" value="Ward" /> | |
375 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" /> | |
376 | |
377 </test> | |
378 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied --> | |
379 </tests> | |
380 </tool> |