Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

comparison mda_advanced_heatmap_gen.xml @ 3:9359e0a0d40b draft

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Uploaded ng-chm version 2.5.3 handles java 8 issue and updates to heatmap viewer
author insilico-bob
date Mon, 05 Nov 2018 11:23:57 -0500
parents 19382473a76b
children d747292c486f
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2:19382473a76b 3:9359e0a0d40b
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="2.5.3">
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="1.8">java</requirement>
5 </requirements> 6 </requirements>
6 <description> Create Clustered Heat Maps with Advanced Options</description> 7 <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_$colTopItems' 8 <command interpreter="bash" detect_errors="aggressive">$__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 9
9 " 10 "
10 #for $attr in $hm_attribute 11 #for $attr in $hm_attribute
11 ${attr.attrbute_key}:${attr.attrbute_value}; 12 '${attr.attrbute_key}':'${attr.attrbute_value}';
12 #end for 13 #end for
13 " 14 "
14 15
15 #for $op in $operations 16 #for $op in $operations
16 ${op.class_name} 17 '${op.class_name}'
17 ${op.repeatinput.file_name} 18 '${op.repeatinput.file_name}'
18 ${op.cattype.cat} 19 '${op.cattype.cat}'
19 ${op.cattype.bartype} 20 '${op.cattype.bartype}'
20 #end for 21 #end for
21 '$output' 22 '$output'
22 </command> 23 </command>
23 <stdio> 24 <stdio>
24 <exit_code range="1:" level="fatal" /> 25 <exit_code range="1:" level="fatal" />