Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

comparison mda_advanced_heatmap_gen.xml @ 6:1f13d304ddbd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author insilico-bob
date Thu, 20 Jun 2019 11:36:53 -0400
parents 15c71ed09efa
children c5489978071a
comparison
equal deleted inserted replaced
5:15c71ed09efa 6:1f13d304ddbd
1 <?xml version="1.0" encoding="UTF-8" ?> 1 <?xml version="1.0" encoding="UTF-8" ?>
2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3"> 2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3">
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.4.1">r-base</requirement> 4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <requirement type="package" version="8">openjdk</requirement> 5 <requirement type="package" version="8.0.144">openjdk</requirement>
6 </requirements> 6 </requirements>
7 <description> Create Clustered Heat Maps with Advanced Options</description> 7 <description> Create Clustered Heat Maps with Advanced Options</description>
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_$colTopItems' 8 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap_advanced.sh "$__tool_directory__" "$__tool_data_path__/" "chm_name|Heat_Map_$hmname" "chm_description|$hmdesc" "summary_width|$summaryDisplayWidth"
9 9 "row_configuration|order_method|${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|${d_rows.rowDendroHeight}"
10 " 10 "col_configuration|order_method|${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 11 #for $attr in $hm_attribute
12 '${attr.attrbute_key}':'${attr.attrbute_value}'; 12 'attribute|${attr.attrbute_key}':'${attr.attrbute_value}'
13 #end for 13 #end for
14 " 14 #for $mx in $matrices
15 15 'matrix_files|path|$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
16 #for $op in $operations 17 #for $op in $operations
17 '${op.class_name}' 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|${op.cattype.scatbar.bg_color}'
18 '${op.repeatinput.file_name}' 19 #end for
19 '${op.cattype.cat}' 20 'output_location|$output'
20 '${op.cattype.bartype}'
21 #end for
22 '$output'
23 </command> 21 </command>
24 <stdio> 22 <stdio>
25 <exit_code range="1:" level="fatal" /> 23 <exit_code range="1:" level="fatal" />
26 </stdio> 24 </stdio>
27 <inputs> 25 <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."/> 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>
29 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> 75 <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> 76 <sanitizer>
31 <valid> 77 <valid>
32 <add preset="string.printable"/> 78 <add preset="string.printable"/>
33 <remove value="&quot;"/> 79 <remove value="&quot;"/>
42 <remove value="&quot;"/> 88 <remove value="&quot;"/>
43 <remove value="&apos;"/> 89 <remove value="&apos;"/>
44 <remove value=" "/> 90 <remove value=" "/>
45 </valid> 91 </valid>
46 </sanitizer> 92 </sanitizer>
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."> 93 <param name="summaryDisplayWidth" type="select" label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel.">
48 <option value="average">Average</option> 94 <option value="50">50%</option>
49 <option value="sample">Sample</option> 95 <option value="10">10%</option>
50 <option value="mode">Mode</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>
51 </param> 103 </param>
52 <conditional name="d_rows"> 104 <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."> 105 <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> 106 <option value="Hierarchical">Hierarchical Clustering</option>
55 <option value="Original">Original Order</option> 107 <option value="Original">Original Order</option>
56 <option value="Random">Random</option> 108 <option value="Random">Random</option>
57 </param> 109 </param>
58 <when value="Hierarchical"> 110 <when value="Hierarchical">
59 <param name="rowDistanceMeasure" type="select" label="Row Distance Metric" help="For clustering, select the method of determining distance between rows."> 111 <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> 112 <option value="euclidean">Euclidean</option>
61 <option value="binary">Binary</option> 113 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
62 <option value="manhattan">Manhattan</option> 114 <option value="manhattan">Manhattan</option>
63 <option value="maximum">Maximum</option> 115 <option value="maximum">Maximum</option>
64 <option value="canberra">Canberra</option> 116 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
65 <option value="minkowski">Minkowski</option> 117 <option value="minkowski">Minkowski</option>
66 <option value="correlation">Correlation</option> 118 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
67 </param> 119 </param>
68 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters."> 120 <param name="rowAgglomerationMethod" type="select" label="Row Clustering Method" help="For clustering, select algorithm for building clusters.">
69 <option value="average">Average Linkage</option> 121 <option value="average">Average Linkage</option>
70 <option value="complete">Complete Linkage</option> 122 <option value="complete">Complete Linkage</option>
71 <option value="single">Single Linkage</option> 123 <option value="single">Single Linkage</option>
72 <option value="ward" selected="true">Ward</option> 124 <option value="ward" selected="true">Ward</option>
73 <option value="mcquitty">Mcquitty</option> 125 <option value="mcquitty">Mcquitty</option>
74 <option value="median">Median</option> 126 <!-- <option value="median">Median</option> ** breaks dendrogram
75 <option value="centroid">Centroid</option> 127 <option value="centroid">Centroid</option> ** breaks dendrogram -->
76 </param> 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>
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."> 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.">
78 <option value="0" selected="true" >None</option> 143 <option value="0" selected="true" >None</option>
79 <option value="2" >2</option> 144 <option value="2" >2</option>
80 <option value="3" >3</option> 145 <option value="3" >3</option>
81 <option value="4" >4</option> 146 <option value="4" >4</option>
95 <when value="none"> 160 <when value="none">
96 <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/> 161 <param name="rowDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
97 </when> 162 </when>
98 <when value="treecuts"> 163 <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." > 164 <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> 165 <option value="0" selected="true" >None</option>
101 <option value="2t" >2</option> 166 <option value="2" >2</option>
102 <option value="3t" >3</option> 167 <option value="3" >3</option>
103 <option value="4t" >4</option> 168 <option value="4" >4</option>
104 <option value="5t" >5</option> 169 <option value="5" >5</option>
105 <option value="6t" >6</option> 170 <option value="6" >6</option>
106 <option value="7t" >7</option> 171 <option value="7" >7</option>
107 <option value="8t" >8</option> 172 <option value="8" >8</option>
108 <option value="9t" >9</option> 173 <option value="9" >9</option>
109 <option value="10t" >10</option> 174 <option value="10" >10</option>
110 </param> 175 </param>
111 </when> 176 </when>
112 <when value="positional"> 177 <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."/> 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."/>
114 </when> 179 </when>
178 <option value="Random">Random</option> 243 <option value="Random">Random</option>
179 </param> 244 </param>
180 <when value="Hierarchical"> 245 <when value="Hierarchical">
181 <param name="columnDistanceMeasure" type="select" label="Column Distance Metric" help="For clustering, select the method of determining distance between columns."> 246 <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> 247 <option value="euclidean">Euclidean</option>
183 <option value="binary">Binary</option> 248 <!-- <option value="binary">Binary</option> ** breaks dendrogram -->
184 <option value="manhattan">Manhattan</option> 249 <option value="manhattan">Manhattan</option>
185 <option value="maximum">Maximum</option> 250 <option value="maximum">Maximum</option>
186 <option value="canberra">Canberra</option> 251 <!-- <option value="canberra">Canberra</option> ** breaks dendrogram -->
187 <option value="minkowski">Minkowski</option> 252 <option value="minkowski">Minkowski</option>
188 <option value="correlation">Correlation</option> 253 <!-- <option value="correlation">Correlation</option> ** breaks dendrogram -->
189 </param> 254 </param>
190 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters."> 255 <param name="columnAgglomerationMethod" type="select" label="Column Clustering Method" help="For clustering, select algorithm for building clusters.">
191 <option value="average">Average Linkage</option> 256 <option value="average">Average Linkage</option>
192 <option value="complete">Complete Linkage</option> 257 <option value="complete">Complete Linkage</option>
193 <option value="single">Single Linkage</option> 258 <option value="single">Single Linkage</option>
194 <option value="ward" selected="true">Ward</option> 259 <option value="ward" selected="true">Ward</option>
195 <option value="mcquitty">Mcquitty</option> 260 <option value="mcquitty">Mcquitty</option>
196 <option value="median">Median</option> 261 <!-- <option value="median">Median</option> ** breaks dendrogram
197 <option value="centroid">Centroid</option> 262 <option value="centroid">Centroid</option> ** breaks dendrogram -->
198 </param> 263 </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."> 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.">
200 <option value="0" selected="true" >None</option> 278 <option value="0" selected="true" >None</option>
201 <option value="2" >2</option> 279 <option value="2" >2</option>
202 <option value="3" >3</option> 280 <option value="3" >3</option>
203 <option value="4" >4</option> 281 <option value="4" >4</option>
204 <option value="5" >5</option> 282 <option value="5" >5</option>
217 <when value="none"> 295 <when value="none">
218 <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/> 296 <param name="colDendroTreeCut" type="text" size="0" hidden="true" value="0"/>
219 </when> 297 </when>
220 <when value="treecuts"> 298 <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."> 299 <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> 300 <option value="0" selected="true" >None</option>
223 <option value="2t" >2</option> 301 <option value="2" >2</option>
224 <option value="3t" >3</option> 302 <option value="3" >3</option>
225 <option value="4t" >4</option> 303 <option value="4" >4</option>
226 <option value="5t" >5</option> 304 <option value="5" >5</option>
227 <option value="6t" >6</option> 305 <option value="6" >6</option>
228 <option value="7t" >7</option> 306 <option value="7" >7</option>
229 <option value="8t" >8</option> 307 <option value="8" >8</option>
230 <option value="9t" >9</option> 308 <option value="9" >9</option>
231 <option value="10t" >10</option> 309 <option value="10" >10</option>
232 </param> 310 </param>
233 </when> 311 </when>
234 <when value="positional"> 312 <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."/> 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."/>
236 </when> 314 </when>
303 <remove value=" "/> 381 <remove value=" "/>
304 </valid> 382 </valid>
305 </sanitizer> 383 </sanitizer>
306 </param> 384 </param>
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."/> 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."/>
308 <conditional name="cattype"> 387 <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."> 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.">
310 <option value="row_categorical" >Row Categorical</option> 389 <option value="row_discrete" >Row Categorical</option>
311 <option value="row_continuous" >Row Continuous</option> 390 <option value="row_continuous" >Row Continuous</option>
312 <option value="column_categorical" >Column Categorical</option> 391 <option value="column_discrete" >Column Categorical</option>
313 <option value="column_continuous" >Column Continuous</option> 392 <option value="column_continuous" >Column Continuous</option>
314 </param> 393 </param>
315 <when value="row_continuous"> 394 <when value="row_continuous">
316 <param name="bartype" type="select" label="Display Type"> 395 <conditional name="scatbar">
317 <option value="color_plot" >Standard</option> 396 <param name="bartype" type="select" label="Display Type">
318 <option value="bar_plot" >Bar Plot</option> 397 <option value="color_plot" >Standard</option>
319 <option value="scatter_plot" >Scatter Plot</option> 398 <option value="bar_plot" >Bar Plot</option>
320 </param> 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>
321 </when> 414 </when>
322 <when value="column_continuous"> 415 <when value="column_continuous">
323 <param name="bartype" type="select" label="Display Type"> 416 <conditional name="scatbar">
324 <option value="color_plot" >Standard</option> 417 <param name="bartype" type="select" label="Display Type">
325 <option value="bar_plot" >Bar Plot</option> 418 <option value="color_plot" >Standard</option>
326 <option value="scatter_plot" >Scatter Plot</option> 419 <option value="bar_plot" >Bar Plot</option>
327 </param> 420 <option value="scatter_plot" >Scatter Plot</option>
328 </when> 421 </param>
329 <when value="column_categorical"> 422 <when value="color_plot">
330 <param name="bartype" type="text" hidden="true" value="color_plot"/> 423 <param name="bg_color" type="text" size="0" hidden="true" value="#ffffff"/>
331 </when> 424 <param name="fg_color" type="text" size="0" hidden="true" value="#000000"/>
332 <when value="row_categorical"> 425 </when>
333 <param name="bartype" type="text" hidden="true" value="color_plot"/> 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>
334 </when> 457 </when>
335 </conditional> 458 </conditional>
336 </repeat> 459 </repeat>
337 <repeat name="hm_attribute" title="Heat Map Attributes"> 460 <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)."> 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).">