Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
comparison mda_advanced_heatmap_gen.xml @ 2:19382473a76b draft
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author | insilico-bob |
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date | Thu, 08 Feb 2018 14:47:49 -0500 |
parents | 603f99d9e776 |
children | 9359e0a0d40b |
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1:603f99d9e776 | 2:19382473a76b |
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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="2.1.1"> | 2 <tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3"> |
3 <description> Create Clustered Heat Maps</description> | 3 <requirements> |
4 <!-- command interpreter="python" detect_errors="aggressive">$__tool_directory__/mad_advanced_heatmap_gen.py 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType --> | 4 <requirement type="package" version="3.4.1">r-base</requirement> |
5 <command interpreter="bash" detect_errors="aggressive">$__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__' ${d_rows.rowDendroCut} ${d_cols.colDendroCut} $rowDataType $colDataType 'c_${d_rows.rcutrows.rowDendroTreeCut}' 'c_${d_cols.ccutrows.colDendroTreeCut}' 't_$rowTopItems' 't_$colTopItems' | 5 </requirements> |
6 <description> Create Clustered Heat Maps with Advanced Options</description> | |
7 <command interpreter="bash" detect_errors="aggressive">$__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' | |
6 | 8 |
7 " | 9 " |
8 #for $attr in $hm_attribute | 10 #for $attr in $hm_attribute |
9 ${attr.attrbute_key}:${attr.attrbute_value}; | 11 ${attr.attrbute_key}:${attr.attrbute_value}; |
10 #end for | 12 #end for |
21 <stdio> | 23 <stdio> |
22 <exit_code range="1:" level="fatal" /> | 24 <exit_code range="1:" level="fatal" /> |
23 </stdio> | 25 </stdio> |
24 <inputs> | 26 <inputs> |
25 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/> | 27 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data."/> |
26 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> | 28 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> |
29 <sanitizer> | |
30 <valid> | |
31 <add preset="string.printable"/> | |
32 <remove value="""/> | |
33 <remove value="'"/> | |
34 <remove value=" "/> | |
35 </valid> | |
36 </sanitizer> | |
27 <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."/> | 37 <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."/> |
38 <sanitizer> | |
39 <valid> | |
40 <add preset="string.printable"/> | |
41 <remove value="""/> | |
42 <remove value="'"/> | |
43 <remove value=" "/> | |
44 </valid> | |
45 </sanitizer> | |
28 <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."> | 46 <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."> |
29 <option value="average">Average</option> | 47 <option value="average">Average</option> |
30 <option value="sample">Sample</option> | 48 <option value="sample">Sample</option> |
31 <option value="mode">Mode</option> | 49 <option value="mode">Mode</option> |
32 </param> | 50 </param> |
273 <option value="scholar" >Scholarly term</option> | 291 <option value="scholar" >Scholarly term</option> |
274 <option value="bio.gene.unigene" >Unigene CId</option> | 292 <option value="bio.gene.unigene" >Unigene CId</option> |
275 <option value="bio.protein.uniprot" >UniProt Id</option> | 293 <option value="bio.protein.uniprot" >UniProt Id</option> |
276 </param> | 294 </param> |
277 <repeat name="operations" title="Covariate Bars"> | 295 <repeat name="operations" title="Covariate Bars"> |
278 <param name="class_name" size="20" type="text" value="" label="Covariate Name" help="Label for the covariate to display in the heat map."> | 296 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label."> |
279 <sanitizer invalid_char="_"> | 297 <sanitizer> |
280 <valid initial="none"> | 298 <valid> |
281 <add preset="string.letters"/> | 299 <add preset="string.printable"/> |
282 <add preset="string.digits"/> | 300 <remove value="""/> |
283 </valid> | 301 <remove value="'"/> |
284 <mapping initial="none"> | 302 <remove value=" "/> |
285 </mapping> | 303 </valid> |
286 </sanitizer> | 304 </sanitizer> |
287 </param> | 305 </param> |
288 <param name="repeatinput" type="data" format="text" label="Covariate File" help="Tab delimited text file with row or column label and covariate value on each line."/> | 306 <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."/> |
289 <conditional name="cattype"> | 307 <conditional name="cattype"> |
290 <param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> | 308 <param name="cat" type="select" label="Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> |
291 <option value="row_categorical" >Row Categorical</option> | 309 <option value="row_categorical" >Row Categorical</option> |
292 <option value="row_continuous" >Row Continuous</option> | 310 <option value="row_continuous" >Row Continuous</option> |
293 <option value="column_categorical" >Column Categorical</option> | 311 <option value="column_categorical" >Column Categorical</option> |