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comparison mda_advanced_heatmap_gen.xml @ 39:436f03b71cf6 draft

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author insilico-bob
date Thu, 20 Jun 2019 11:31:24 -0400
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38:605ec840a06b 39:436f03b71cf6
1 <?xml version="1.0" encoding="UTF-8" ?>
2 <tool id="mda_advanced_heatmap_gen" name="Advanced 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 with Advanced Options</description>
8 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" "summary_width|$summaryDisplayWidth"
9 "row_configuration|order_method|${d_rows.rowOrderMethod}|distance_metric|${d_rows.rowDistanceMeasure}|agglomeration_method|${d_rows.rowAgglomerationMethod}|tree_covar_cuts|${d_rows.rowDendroCut}|data_type|$rowDataType|top_items|$rowTopItems|tree_cuts|${d_rows.rcutrows.rowDendroTreeCut}|${d_rows.rcutrows.raddcuts}|dendro_show|${d_rows.rowDendroShow}|dendro_height|${d_rows.rowDendroHeight}"
10 "col_configuration|order_method|${d_cols.columnOrderMethod}|distance_metric|${d_cols.columnDistanceMeasure}|agglomeration_method|${d_cols.columnAgglomerationMethod}|tree_covar_cuts|${d_cols.colDendroCut}|data_type|$colDataType|top_items|$colTopItems|tree_cuts|${d_cols.ccutrows.colDendroTreeCut}|${d_cols.ccutrows.caddcuts}|dendro_show|${d_cols.columnDendroShow}|dendro_height|${d_cols.columnDendroHeight}"
11 #for $attr in $hm_attribute
12 'attribute|${attr.attrbute_key}':'${attr.attrbute_value}'
13 #end for
14 #for $mx in $matrices
15 'matrix_files|path|$mx.dataLayer|name|${mx.dataLayerName}|summary_method|${mx.summarymethod}|selection_color|${mx.dataLayerSelectionColor}|cuts_color|${mx.dataLayerCutsColor}|grid_color|${mx.dataLayerGridColor}|grid_show|${mx.dataLayerGridShow}|${mx.colorsBreaks.setColorsBreaks}|${mx.colorsBreaks.matrixColor1}|${mx.colorsBreaks.matrixColor2}|${mx.colorsBreaks.matrixColor3}|${mx.colorsBreaks.matrixBreak1}|${mx.colorsBreaks.matrixBreak2}|${mx.colorsBreaks.matrixBreak3}|${mx.colorsBreaks.missingColor}'
16 #end for
17 #for $op in $operations
18 'classification|name|${op.class_name}|path|${op.repeatinput.file_name}|category|${op.cattype.cat}|bar_type|${op.cattype.scatbar.bartype}|height|${op.classHeight}|fg_color|${op.cattype.scatbar.fg_color}|bg_color|${op.cattype.scatbar.bg_color}'
19 #end for
20 'output_location|$output'
21 </command>
22 <stdio>
23 <exit_code range="1:" level="fatal" />
24 </stdio>
25 <inputs>
26 <repeat name="matrices" title="Heat Map Matrices">
27 <param name="dataLayer" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/>
28 <param name="dataLayerName" size="40" type="text" value="Data_Layer_name" label="Data Layer Name" help="Name for data layer (no spaces).">
29 <sanitizer>
30 <valid>
31 <add preset="string.printable"/>
32 <remove value="&quot;"/>
33 <remove value="&apos;"/>
34 <remove value=" "/>
35 </valid>
36 </sanitizer>
37 </param>
38 <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.">
39 <option value="average">Average</option>
40 <option value="sample">Sample</option>
41 <option value="mode">Mode</option>
42 </param>
43 <conditional name="colorsBreaks">
44 <param name="setColorsBreaks" type="select" label="Colors and Breakpoints" help="Select whether to set your own colors and breakpoints or use default values.">
45 <option value="none">Use System Generated Colors and Breakpoints</option>
46 <option value="defined">Define Your Own Colors and Breakpoints</option>
47 </param>
48 <when value="none">
49 <param name="matrixColor1" type="text" size="0" hidden="true" value="0"/>
50 <param name="matrixBreak1" type="text" size="0" hidden="true" value="0"/>
51 <param name="matrixColor2" type="text" size="0" hidden="true" value="0"/>
52 <param name="matrixBreak2" type="text" size="0" hidden="true" value="0"/>
53 <param name="matrixColor3" type="text" size="0" hidden="true" value="0"/>
54 <param name="matrixBreak3" type="text" size="0" hidden="true" value="0"/>
55 <param name="missingColor" type="text" size="0" hidden="true" value="0"/>
56 </when>
57 <when value="defined">
58 <param name="matrixColor1" type="color" label="Color for Breakpoint One" value="#ff0000"/>
59 <param name="matrixBreak1" type="text" label="Value for Breakpoint One" value="-1"/>
60 <param name="matrixColor2" type="color" label="Color for Breakpoint Two" value="#ffffff"/>
61 <param name="matrixBreak2" type="text" label="Value for Breakpoint Two" value="0"/>
62 <param name="matrixColor3" type="color" label="Color for Breakpoint Three" value="#0000ff"/>
63 <param name="matrixBreak3" type="text" label="Value for Breakpoint Three" value="1"/>
64 <param name="missingColor" type="color" label="Color for Missing Values" value="#000000"/>
65 </when>
66 </conditional>
67 <param name="dataLayerSelectionColor" type="color" label="Color for selection box" value="#00ff38"/>
68 <param name="dataLayerCutsColor" type="color" label="Color for Heat Map Gaps" value="#ffffff"/>
69 <param name="dataLayerGridColor" type="color" label="Color for Heat Map Grid" value="#ffffff"/>
70 <param name="dataLayerGridShow" type="select" label="Show Heat Map Grid">
71 <option value="Y">Yes</option>
72 <option value="N">No</option>
73 </param>
74 </repeat>
75 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
76 <sanitizer>
77 <valid>
78 <add preset="string.printable"/>
79 <remove value="&quot;"/>
80 <remove value="&apos;"/>
81 <remove value=" "/>
82 </valid>
83 </sanitizer>
84 <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."/>
85 <sanitizer>
86 <valid>
87 <add preset="string.printable"/>
88 <remove value="&quot;"/>
89 <remove value="&apos;"/>
90 <remove value=" "/>
91 </valid>
92 </sanitizer>
93 <param name="summaryDisplayWidth" type="select" label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel.">
94 <option value="50">50%</option>
95 <option value="10">10%</option>
96 <option value="20">20%</option>
97 <option value="30">30%</option>
98 <option value="40">40%</option>
99 <option value="60">60%</option>
100 <option value="70">70%</option>
101 <option value="80">80%</option>
102 <option value="90">90%</option>
103 </param>
104 <conditional name="d_rows">
105 <param name="rowOrderMethod" type="select" label="Row ordering method" help="Determine if rows should be clustered, randomized, or remain as is.">
106 <option value="Hierarchical">Hierarchical Clustering</option>
107 <option value="Original">Original Order</option>
108 <option value="Random">Random</option>
109 </param>
110 <when value="Hierarchical">
111 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows.">
112 <option value="euclidean">Euclidean</option>
113 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
114 <option value="manhattan">Manhattan</option>
115 <option value="maximum">Maximum</option>
116 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
117 <option value="minkowski">Minkowski</option>
118 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
119 </param>
120 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
121 <option value="average">Average Linkage</option>
122 <option value="complete">Complete Linkage</option>
123 <option value="single">Single Linkage</option>
124 <option value="ward" selected="true">Ward</option>
125 <option value="mcquitty">Mcquitty</option>
126 <!-- <option value="median">Median</option> ** breaks dendrogram
127 <option value="centroid">Centroid</option> ** breaks dendrogram -->
128 </param>
129 <param name="rowDendroShow" type="select" label="Show Row Dendrogram" help="For setting the visibility of the row dendrogram.">
130 <option value="ALL">Summary and Detail</option>
131 <option value="SUMMARY">Summary Only</option>
132 <option value="NONE">Hide</option>
133 </param>
134 <param name="rowDendroHeight" type="select" label="Row Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
135 <option value="100">100%</option>
136 <option value="50">50%</option>
137 <option value="75">75%</option>
138 <option value="125">125%</option>
139 <option value="150">150%</option>
140 <option value="200">200%</option>
141 </param>
142 <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.">
143 <option value="0" selected="true" >None</option>
144 <option value="2" >2</option>
145 <option value="3" >3</option>
146 <option value="4" >4</option>
147 <option value="5" >5</option>
148 <option value="6" >6</option>
149 <option value="7" >7</option>
150 <option value="8" >8</option>
151 <option value="9" >9</option>
152 <option value="10" >10</option>
153 </param>
154 <conditional name="rcutrows">
155 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
156 <option value="none">None</option>
157 <option value="treecuts">Cluster-Based Gaps</option>
158 <option value="positional">Fixed Gaps</option>
159 </param>
160 <when value="none">
161 <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
162 </when>
163 <when value="treecuts">
164 <param name="rowDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters." >
165 <option value="0" selected="true" >None</option>
166 <option value="2" >2</option>
167 <option value="3" >3</option>
168 <option value="4" >4</option>
169 <option value="5" >5</option>
170 <option value="6" >6</option>
171 <option value="7" >7</option>
172 <option value="8" >8</option>
173 <option value="9" >9</option>
174 <option value="10" >10</option>
175 </param>
176 </when>
177 <when value="positional">
178 <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."/>
179 </when>
180 </conditional>
181 </when>
182 <when value="Original">
183 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
184 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
185 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
186 <conditional name="rcutrows">
187 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
188 <option value="none">None</option>
189 <option value="positional">Fixed Gaps</option>
190 </param>
191 <when value="none">
192 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
193 </when>
194 <when value="positional">
195 <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."/>
196 </when>
197 </conditional>
198 </when>
199 <when value="Random">
200 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
201 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
202 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
203 <conditional name="rcutrows">
204 <param name="raddcuts" type="select" label="Add row gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
205 <option value="none">None</option>
206 <option value="positional">Fixed Gaps</option>
207 </param>
208 <when value="none">
209 <param name="rowDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
210 </when>
211 <when value="positional">
212 <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."/>
213 </when>
214 </conditional>
215 </when>
216 </conditional>
217 <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."/>
218 <param name="rowDataType" type="select" label="Row Label Type" help="Enable label driven link-outs by specifying the type of row labels.">
219 <option value="labels" selected="true" >None</option>
220 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
221 <option value="bio.feature.agilent" >Agilent Id</option>
222 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
223 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
224 <option value="bio.gene.entrez" >Gene Entrez Id</option>
225 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
226 <option value="bio.go" >Gene Ontology (GO) Id</option>
227 <option value="bio.geo.acc" >GEO Accession Id</option>
228 <option value="bio.probe.illumina" >Illumina Probe Id</option>
229 <option value="bio.probe.infinium" >Infinium Probe Id</option>
230 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
231 <option value="bio.mirna" >miRNA Id</option>
232 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
233 <option value="bio.pubmed" >Pubmed Id</option>
234 <option value="bio.pubmed.search" >Pubmed Search Term</option>
235 <option value="scholar" >Scholarly term</option>
236 <option value="bio.gene.unigene" >Unigene CId</option>
237 <option value="bio.protein.uniprot" >UniProt Id</option>
238 </param>
239 <conditional name="d_cols">
240 <param name="columnOrderMethod" type="select" label="Column ordering method" help="Determine if columns should be clustered, randomized, or remain as is.">
241 <option value="Hierarchical">Hierarchical Clustering</option>
242 <option value="Original">Original Order</option>
243 <option value="Random">Random</option>
244 </param>
245 <when value="Hierarchical">
246 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns.">
247 <option value="euclidean">Euclidean</option>
248 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
249 <option value="manhattan">Manhattan</option>
250 <option value="maximum">Maximum</option>
251 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
252 <option value="minkowski">Minkowski</option>
253 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
254 </param>
255 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
256 <option value="average">Average Linkage</option>
257 <option value="complete">Complete Linkage</option>
258 <option value="single">Single Linkage</option>
259 <option value="ward" selected="true">Ward</option>
260 <option value="mcquitty">Mcquitty</option>
261 <!-- <option value="median">Median</option> ** breaks dendrogram
262 <option value="centroid">Centroid</option> ** breaks dendrogram -->
263 </param>
264 <param name="columnDendroShow" type="select" label="Show Column Dendrogram" help="For setting the visibility of the column dendrogram.">
265 <option value="ALL">Summary and Detail</option>
266 <option value="SUMMARY">Summary Only</option>
267 <option value="NONE">Hide</option>
268 </param>
269 <param name="columnDendroHeight" type="select" label="Column Dendrogram Display Height" help="For adjusting the displayed height of the dendrogram bar.">
270 <option value="100">100%</option>
271 <option value="50">50%</option>
272 <option value="75">75%</option>
273 <option value="125">125%</option>
274 <option value="150">150%</option>
275 <option value="200">200%</option>
276 </param>
277 <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.">
278 <option value="0" selected="true" >None</option>
279 <option value="2" >2</option>
280 <option value="3" >3</option>
281 <option value="4" >4</option>
282 <option value="5" >5</option>
283 <option value="6" >6</option>
284 <option value="7" >7</option>
285 <option value="8" >8</option>
286 <option value="9" >9</option>
287 <option value="10" >10</option>
288 </param>
289 <conditional name="ccutrows">
290 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
291 <option value="none">None</option>
292 <option value="treecuts">Cluster-Based Gaps</option>
293 <option value="positional">Fixed Gaps</option>
294 </param>
295 <when value="none">
296 <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
297 </when>
298 <when value="treecuts">
299 <param name="colDendroTreeCut" type="select" label="Cluster-Based Gap" help="Gaps will be placed between clusters. Select the number of clusters.">
300 <option value="0" selected="true" >None</option>
301 <option value="2" >2</option>
302 <option value="3" >3</option>
303 <option value="4" >4</option>
304 <option value="5" >5</option>
305 <option value="6" >6</option>
306 <option value="7" >7</option>
307 <option value="8" >8</option>
308 <option value="9" >9</option>
309 <option value="10" >10</option>
310 </param>
311 </when>
312 <when value="positional">
313 <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."/>
314 </when>
315 </conditional>
316 </when>
317 <when value="Original">
318 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
319 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
320 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
321 <conditional name="ccutrows">
322 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
323 <option value="none">None</option>
324 <option value="positional">Fixed Gaps</option>
325 </param>
326 <when value="none">
327 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
328 </when>
329 <when value="positional">
330 <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."/>
331 </when>
332 </conditional>
333 </when>
334 <when value="Random">
335 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
336 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
337 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
338 <conditional name="ccutrows">
339 <param name="caddcuts" type="select" label="Add column gap(s)" help="To separate portions of the heat map with gaps, select a gap method.">
340 <option value="none">None</option>
341 <option value="positional">Fixed Gaps</option>
342 </param>
343 <when value="none">
344 <param name="colDendroTreeCut" type="text" size="100" value="None" hidden="true"/>
345 </when>
346 <when value="positional">
347 <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."/>
348 </when>
349 </conditional>
350 </when>
351 </conditional>
352 <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."/>
353 <param name="colDataType" type="select" label="Column Label Type" help="Enable label driven link-outs by specifying the type of column labels.">
354 <option value="labels" selected="true" >None</option>
355 <option value="bio.probe.affymetrix" >Affymetrix Probe Id</option>
356 <option value="bio.feature.agilent" >Agilent Id</option>
357 <option value="bio.sample.cbioportal" >cBioPortal sample Id</option>
358 <option value="bio.transcript.ensemble" >Ensemble transcript Id</option>
359 <option value="bio.gene.entrez" >Gene Entrez Id</option>
360 <option value="bio.gene.hugo" >Gene HUGO symbol</option>
361 <option value="bio.go" >Gene Ontology (GO) Id</option>
362 <option value="bio.geo.acc" >GEO Accession Id</option>
363 <option value="bio.probe.illumina" >Illumina Probe Id</option>
364 <option value="bio.probe.infinium" >Infinium Probe Id</option>
365 <option value="bio.pathway.mdanderson" >MD Anderson pathway Id</option>
366 <option value="bio.mirna" >miRNA Id</option>
367 <option value="bio.mirna.mimat" >miRNA MIMAT Id</option>
368 <option value="bio.pubmed" >Pubmed Id</option>
369 <option value="bio.pubmed.search" >Pubmed Search Term</option>
370 <option value="scholar" >Scholarly term</option>
371 <option value="bio.gene.unigene" >Unigene CId</option>
372 <option value="bio.protein.uniprot" >UniProt Id</option>
373 </param>
374 <repeat name="operations" title="Covariate Bars">
375 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
376 <sanitizer>
377 <valid>
378 <add preset="string.printable"/>
379 <remove value="&quot;"/>
380 <remove value="&apos;"/>
381 <remove value=" "/>
382 </valid>
383 </sanitizer>
384 </param>
385 <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."/>
386 <param name="classHeight" size="10" type="text" value="15" label="Covariate Display Height" help="Set the display height for column covariates and width for row covariates."/>
387 <conditional name="cattype">
388 <param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
389 <option value="row_discrete" >Row Categorical</option>
390 <option value="row_continuous" >Row Continuous</option>
391 <option value="column_discrete" >Column Categorical</option>
392 <option value="column_continuous" >Column Continuous</option>
393 </param>
394 <when value="row_continuous">
395 <conditional name="scatbar">
396 <param name="bartype" type="select" label="Display Type">
397 <option value="color_plot" >Standard</option>
398 <option value="bar_plot" >Bar Plot</option>
399 <option value="scatter_plot" >Scatter Plot</option>
400 </param>
401 <when value="color_plot">
402 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
403 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
404 </when>
405 <when value="bar_plot">
406 <param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
407 <param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
408 </when>
409 <when value="scatter_plot">
410 <param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
411 <param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
412 </when>
413 </conditional>
414 </when>
415 <when value="column_continuous">
416 <conditional name="scatbar">
417 <param name="bartype" type="select" label="Display Type">
418 <option value="color_plot" >Standard</option>
419 <option value="bar_plot" >Bar Plot</option>
420 <option value="scatter_plot" >Scatter Plot</option>
421 </param>
422 <when value="color_plot">
423 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
424 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
425 </when>
426 <when value="bar_plot">
427 <param name="bg_color" type="color" label="Color for Bar Plot Background" value="#ffffff"/>
428 <param name="fg_color" type="color" label="Color for Bar Plot Foreground" value="#000000"/>
429 </when>
430 <when value="scatter_plot">
431 <param name="bg_color" type="color" label="Color for Scatter Plot Background" value="#ffffff"/>
432 <param name="fg_color" type="color" label="Color for Scatter Plot Foreground" value="#000000"/>
433 </when>
434 </conditional>
435 </when>
436 <when value="column_discrete">
437 <conditional name="scatbar">
438 <param name="bartype" type="select" hidden="true">
439 <option value="color_plot" >Standard</option>
440 </param>
441 <when value="color_plot">
442 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
443 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
444 </when>
445 </conditional>
446 </when>
447 <when value="row_discrete">
448 <conditional name="scatbar">
449 <param name="bartype" type="select" hidden="true">
450 <option value="color_plot" >Standard</option>
451 </param>
452 <when value="color_plot">
453 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
454 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
455 </when>
456 </conditional>
457 </when>
458 </conditional>
459 </repeat>
460 <repeat name="hm_attribute" title="Heat Map Attributes">
461 <param name="attrbute_key" size="50" type="text" value="" label="Heat Map Attribute Key" help="For map level attributes. Enter the key (no spaces).">
462 <sanitizer invalid_char="_">
463 <valid initial="">
464 <add preset="string.letters"/>
465 <add preset="string.digits"/>
466 </valid>
467 <mapping initial="">
468 </mapping>
469 </sanitizer>
470 </param>
471 <param name="attrbute_value" size="50" type="text" label="Heat Map Attributes Value" help="For map level attributes. Enter the value (no spaces).">
472 <sanitizer invalid_char="_">
473 <valid initial="">
474 <add preset="string.letters"/>
475 <add preset="string.digits"/>
476 </valid>
477 <mapping initial="">
478 </mapping>
479 </sanitizer>
480 </param>
481 </repeat>
482 </inputs>
483 <outputs>
484 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>
485 </outputs>
486 <tests>
487 <test>
488 <param name="inputmatrix" value="400x400.txt" />
489 <param name="hmname" value="testRun" />
490 <param name="$hmdesc" value="validateTool" />
491 <param name="summarymethod" value="Average" />
492 <param name="rowOrderMethod" value="Hierarchical" />
493 <param name="rowDistanceMeasure" value="Manhattan" />
494 <param name="rowAgglomerationMethod" value="Ward" />
495 <param name="columnOrderMethod" value="Hierarchical" />
496 <param name="columnDistanceMeasure" value="Manhattan" />
497 <param name="columnAgglomerationMethod" value="Ward" />
498 <output name="output" file="Galaxy400x400-noCovariates.ngchm" lines_diff="10" />
499
500 </test>
501 <!-- galaxy/test-data/ dir where the input and output file that should match tool output will be copied -->
502 </tests>
503 </tool>