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 |
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date | Tue, 28 Jan 2020 15:33:09 -0500 |
parents | 1f13d304ddbd |
children | c1be063b2454 |
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6:1f13d304ddbd | 7:c5489978071a |
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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="""/> | 31 <remove value="""/> |
33 <remove value="'"/> | 32 <remove value="'"/> |
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="""/> | 76 <remove value="""/> |
80 <remove value="'"/> | 77 <remove value="'"/> |
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="""/> | 83 <remove value="""/> |
89 <remove value="'"/> | 84 <remove value="'"/> |
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="""/> | 380 <remove value="""/> |
380 <remove value="'"/> | 381 <remove value="'"/> |
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="""/> | |
390 <remove value="'"/> | |
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="""/> |
465 <add preset="string.digits"/> | 472 <remove value="'"/> |
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="""/> |
475 <add preset="string.digits"/> | 480 <remove value="'"/> |
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"/> |