Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

comparison mda_advanced_heatmap_gen.xml @ 7:c5489978071a draft

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author insilico-bob
date Tue, 28 Jan 2020 15:33:09 -0500
parents 1f13d304ddbd
children c1be063b2454
comparison
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6:1f13d304ddbd 7:c5489978071a
24 </stdio> 24 </stdio>
25 <inputs> 25 <inputs>
26 <repeat name="matrices" title="Heat Map Matrices"> 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."/> 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)."> 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> 29 <sanitizer>
30 <valid> 30 <valid initial="string.printable">
31 <add preset="string.printable"/>
32 <remove value="&quot;"/> 31 <remove value="&quot;"/>
33 <remove value="&apos;"/> 32 <remove value="&apos;"/>
34 <remove value=" "/>
35 </valid> 33 </valid>
36 </sanitizer> 34 </sanitizer>
37 </param> 35 </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."> 36 <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> 37 <option value="average">Average</option>
40 <option value="sample">Sample</option> 38 <option value="sample">Sample</option>
41 <option value="mode">Mode</option> 39 <option value="mode">Mode</option>
71 <option value="Y">Yes</option> 69 <option value="Y">Yes</option>
72 <option value="N">No</option> 70 <option value="N">No</option>
73 </param> 71 </param>
74 </repeat> 72 </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)."/> 73 <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> 74 <sanitizer>
77 <valid> 75 <valid initial="string.printable">
78 <add preset="string.printable"/>
79 <remove value="&quot;"/> 76 <remove value="&quot;"/>
80 <remove value="&apos;"/> 77 <remove value="&apos;"/>
81 <remove value=" "/>
82 </valid> 78 </valid>
83 </sanitizer> 79 </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."/> 80 <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> 81 <sanitizer>
86 <valid> 82 <valid initial="string.printable">
87 <add preset="string.printable"/>
88 <remove value="&quot;"/> 83 <remove value="&quot;"/>
89 <remove value="&apos;"/> 84 <remove value="&apos;"/>
90 <remove value=" "/>
91 </valid> 85 </valid>
92 </sanitizer> 86 </sanitizer>
93 <param name="summaryDisplayWidth" type="select" label="Summary Display Width %" help="Sets the percentage of the viewer display of the summary panel."> 87 <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> 88 <option value="50">50%</option>
95 <option value="10">10%</option> 89 <option value="10">10%</option>
96 <option value="20">20%</option> 90 <option value="20">20%</option>
97 <option value="30">30%</option> 91 <option value="30">30%</option>
181 </when> 175 </when>
182 <when value="Original"> 176 <when value="Original">
183 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> 177 <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"/> 178 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
185 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> 179 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
180 <param name="rowDendroShow" type="text" size="0" hidden="true" value="ALL"/>
181 <param name="rowDendroHeight" type="text" size="0" hidden="true" value="0"/>
186 <conditional name="rcutrows"> 182 <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."> 183 <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> 184 <option value="none">None</option>
189 <option value="positional">Fixed Gaps</option> 185 <option value="positional">Fixed Gaps</option>
190 </param> 186 </param>
198 </when> 194 </when>
199 <when value="Random"> 195 <when value="Random">
200 <param name="rowDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> 196 <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"/> 197 <param name="rowAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
202 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/> 198 <param name="rowDendroCut" type="text" size="0" hidden="true" value="0"/>
199 <param name="rowDendroShow" type="text" size="0" hidden="true" value="ALL"/>
200 <param name="rowDendroHeight" type="text" size="0" hidden="true" value="0"/>
203 <conditional name="rcutrows"> 201 <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."> 202 <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> 203 <option value="none">None</option>
206 <option value="positional">Fixed Gaps</option> 204 <option value="positional">Fixed Gaps</option>
207 </param> 205 </param>
316 </when> 314 </when>
317 <when value="Original"> 315 <when value="Original">
318 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> 316 <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"/> 317 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
320 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/> 318 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
319 <param name="columnDendroShow" type="text" size="0" hidden="true" value="ALL"/>
320 <param name="columnDendroHeight" type="text" size="0" hidden="true" value="0"/>
321 <conditional name="ccutrows"> 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."> 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> 323 <option value="none">None</option>
324 <option value="positional">Fixed Gaps</option> 324 <option value="positional">Fixed Gaps</option>
325 </param> 325 </param>
333 </when> 333 </when>
334 <when value="Random"> 334 <when value="Random">
335 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> 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"/> 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"/> 337 <param name="colDendroCut" type="text" size="0" hidden="true" value="0"/>
338 <param name="columnDendroShow" type="text" size="0" hidden="true" value="ALL"/>
339 <param name="columnDendroHeight" type="text" size="0" hidden="true" value="0"/>
338 <conditional name="ccutrows"> 340 <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."> 341 <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> 342 <option value="none">None</option>
341 <option value="positional">Fixed Gaps</option> 343 <option value="positional">Fixed Gaps</option>
342 </param> 344 </param>
371 <option value="bio.gene.unigene" >Unigene CId</option> 373 <option value="bio.gene.unigene" >Unigene CId</option>
372 <option value="bio.protein.uniprot" >UniProt Id</option> 374 <option value="bio.protein.uniprot" >UniProt Id</option>
373 </param> 375 </param>
374 <repeat name="operations" title="Covariate Bars"> 376 <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."> 377 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
376 <sanitizer> 378 <sanitizer>
377 <valid> 379 <valid initial="string.printable">
378 <add preset="string.printable"/>
379 <remove value="&quot;"/> 380 <remove value="&quot;"/>
380 <remove value="&apos;"/> 381 <remove value="&apos;"/>
381 <remove value=" "/>
382 </valid> 382 </valid>
383 </sanitizer> 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 <sanitizer>
388 <valid initial="string.digits">
389 <remove value="&quot;"/>
390 <remove value="&apos;"/>
391 </valid>
392 </sanitizer>
384 </param> 393 </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"> 394 <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."> 395 <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> 396 <option value="row_discrete" >Row Categorical</option>
390 <option value="row_continuous" >Row Continuous</option> 397 <option value="row_continuous" >Row Continuous</option>
391 <option value="column_discrete" >Column Categorical</option> 398 <option value="column_discrete" >Column Categorical</option>
457 </when> 464 </when>
458 </conditional> 465 </conditional>
459 </repeat> 466 </repeat>
460 <repeat name="hm_attribute" title="Heat Map Attributes"> 467 <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)."> 468 <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="_"> 469 <sanitizer>
463 <valid initial=""> 470 <valid initial="string.printable">
464 <add preset="string.letters"/> 471 <remove value="&quot;"/>
465 <add preset="string.digits"/> 472 <remove value="&apos;"/>
466 </valid> 473 </valid>
467 <mapping initial=""> 474 </sanitizer>
468 </mapping>
469 </sanitizer>
470 </param> 475 </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)."> 476 <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="_"> 477 <sanitizer>
473 <valid initial=""> 478 <valid initial="string.printable">
474 <add preset="string.letters"/> 479 <remove value="&quot;"/>
475 <add preset="string.digits"/> 480 <remove value="&apos;"/>
476 </valid> 481 </valid>
477 <mapping initial=""> 482 </sanitizer>
478 </mapping>
479 </sanitizer>
480 </param> 483 </param>
481 </repeat> 484 </repeat>
482 </inputs> 485 </inputs>
483 <outputs> 486 <outputs>
484 <data name="output" label='Heat_Map_$hmname' format="ngchm"/> 487 <data name="output" label='Heat_Map_$hmname' format="ngchm"/>