Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

diff 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
line wrap: on
line diff
--- a/mda_advanced_heatmap_gen.xml	Thu Feb 08 14:47:49 2018 -0500
+++ b/mda_advanced_heatmap_gen.xml	Mon Nov 05 11:23:57 2018 -0500
@@ -1,22 +1,23 @@
 <?xml version="1.0" encoding="UTF-8" ?>
-<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.3">
+<tool id="mda_advanced_heatmap_gen" name="Advanced NG-CHM Generator" version="2.5.3">
   <requirements>
     <requirement type="package" version="3.4.1">r-base</requirement> 
+	 <requirement type="package" version="1.8">java</requirement>
   </requirements>
   <description> Create Clustered Heat Maps with Advanced Options</description>
-<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_$colTopItems' 
+  <command interpreter="bash" detect_errors="aggressive">$__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' 
 
     "
     #for $attr in $hm_attribute
-      ${attr.attrbute_key}:${attr.attrbute_value};
+      '${attr.attrbute_key}':'${attr.attrbute_value}';
     #end for
     "
 
     #for $op in $operations
-       ${op.class_name}
-       ${op.repeatinput.file_name}
-       ${op.cattype.cat}
-       ${op.cattype.bartype}
+       '${op.class_name}'
+       '${op.repeatinput.file_name}'
+       '${op.cattype.cat}'
+       '${op.cattype.bartype}'
       #end for
  	'$output' 
  </command>