Mercurial > repos > md-anderson-bioinformatics > heat_map_creation

comparison mda_heatmap_gen.xml @ 34:58437af2d675 draft

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author insilico-bob
date Thu, 08 Feb 2018 14:45:46 -0500
parents 0097750ad7ad
children 6ad3c487987d
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33:0097750ad7ad 34:58437af2d675
1 <?xml version="1.0" encoding="UTF-8" ?> 1 <?xml version="1.0" encoding="UTF-8" ?>
2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.1.1"> 2 <tool id="mda_heatmap_gen" name="NG-CHM Generator" version="2.3">
3 <description>Create Clustered Heat Maps</description> 3 <requirements>
4 <!-- <command interpreter="python" detect_errors="aggressive">$__tool_directory__/mda_heatmap_gen.py 'Heat_Map_$hmname' '$hmdesc' '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__' 0 0 labels labels 'None'--> 4 <requirement type="package" version="3.4.1">r-base</requirement>
5 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "standard" "Heat_Map_$hmname" "$hmdesc" '$inputmatrix' ${d_rows.rowOrderMethod} ${d_rows.rowDistanceMeasure} ${d_rows.rowAgglomerationMethod} ${d_cols.columnOrderMethod} ${d_cols.columnDistanceMeasure} ${d_cols.columnAgglomerationMethod} $summarymethod '$__tool_directory__/' 0 0 labels labels 'None' 5 </requirements>
6 <description>Create Clustered Heat Maps</description>
7 <command interpreter="bash" detect_errors="aggressive">$__tool_directory__/heatmap.sh "standard" "Heat_Map_$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__/' 0 0 labels labels 'None'
6 #for $op in $operations 8 #for $op in $operations
7 ${op.class_name} 9 ${op.class_name}
8 ${op.repeatinput.file_name} 10 ${op.repeatinput.file_name}
9 ${op.cat} 11 ${op.cat}
10 #end for 12 #end for
13 <stdio> 15 <stdio>
14 <exit_code range="1:" level="fatal" /> 16 <exit_code range="1:" level="fatal" />
15 </stdio> 17 </stdio>
16 <inputs> 18 <inputs>
17 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data." /> 19 <param name="inputmatrix" type="data" format="Tabular" label="Input Data Matrix" help="Tab delimited text file with row labels, column labels, and data." />
18 <param name="hmname" size="20" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/> 20 <param name="hmname" size="40" type="text" value="Heat_Map_name" label="Heat Map Name" help="Short Name for heat map (no spaces)."/>
21 <sanitizer>
22 <valid>
23 <add preset="string.printable"/>
24 <!-- <add value="string.letters"/>
25 <add value="string.digits"/>
26 <add value="-"/>
27 <add value="_"/>
28 -->
29 <remove value="&quot;"/>
30 <remove value="&apos;"/>
31 <remove value=" "/>
32 </valid>
33 </sanitizer>
19 <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."/> 34 <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."/>
35 <sanitizer>
36 <valid>
37 <add preset="string.printable"/>
38 <add value="string.letters"/>
39 <add value="string.digits"/>
40 <add value="-"/>
41 <add value="_"/>
42 <remove value="&quot;"/>
43 <remove value="&apos;"/>
44 <remove value=" "/>
45 </valid>
46 </sanitizer>
20 <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."> 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.">
21 <option value="average">Average</option> 48 <option value="average">Average</option>
22 <option value="sample">Sample</option> 49 <option value="sample">Sample</option>
23 <option value="mode">Mode</option> 50 <option value="mode">Mode</option>
24 </param> 51 </param>
91 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/> 118 <param name="columnDistanceMeasure" type="text" size="0" hidden="true" value="n/a"/>
92 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/> 119 <param name="columnAgglomerationMethod" type="text" size="0" hidden="true" value="n/a"/>
93 </when> 120 </when>
94 </conditional> 121 </conditional>
95 <repeat name="operations" title="Covariate Bars"> 122 <repeat name="operations" title="Covariate Bars">
96 <param name="class_name" size="20" type="text" value="" label="Covariate Name" help="Label for the covariate to display in the heat map."> 123 <param name="class_name" size="25" type="text" value="" label="Covariate Name" help="Covariate heat map display label.">
97 <sanitizer invalid_char="_"> 124 <sanitizer>
98 <valid initial="none"> 125 <valid>
99 <add preset="string.letters"/> 126 <add preset="string.printable"/>
100 <add preset="string.digits"/> 127 <remove value="&quot;"/>
128 <remove value="&apos;"/>
129 <remove value=" "/>
101 </valid> 130 </valid>
102 <mapping initial="none">
103 </mapping>
104 </sanitizer> 131 </sanitizer>
105 </param> 132 </param>
106 <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."/> 133 <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."/>
107 <param name="cat" type="select" label="Axis Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values."> 134 <param name="cat" type="select" label="Axis Covariate Type" help="Identify the covariate as belonging to rows or columns and containing categorical or continuous values.">
108 <option value="row_categorical" >Row Categorical</option> 135 <option value="row_categorical" >Row Categorical</option>
109 <option value="row_continuous" >Row Continuous</option> 136 <option value="row_continuous" >Row Continuous</option>
110 <option value="column_categorical" >Column Categorical</option> 137 <option value="column_categorical" >Column Categorical</option>
111 <option value="column_continuous" >Column Continuous</option> 138 <option value="column_continuous" >Column Continuous</option>