# HG changeset patch
# User george-weingart
# Date 1409862891 14400
# Node ID 5ecece9f42dd3a8dcbf3db6740974b1b7368966f
# Parent  65bf0d7f535bbccfa06ed1240419aeddbb8f99a3
Uploaded

diff -r 65bf0d7f535b -r 5ecece9f42dd export2graphlan.xml
--- a/export2graphlan.xml	Thu Sep 04 16:19:09 2014 -0400
+++ b/export2graphlan.xml	Thu Sep 04 16:34:51 2014 -0400
@@ -28,6 +28,9 @@
 	--max_font_size  $max_font_size 
         --annotation_legend_font_size $annotation_legend_font_size
 	--abundance_threshold $abundance_threshold
+	#if  $most_abundant  > 0:
+               	--most_abundant  $most_abundant
+	#end if
 	--skip_rows 1,2 
    </command>
    
@@ -49,8 +52,9 @@
 	    	<param name="max_font_size"  type="integer" size="4" value="12"   label="Maximum font size "/>
 	    	<param name="annotation_legend_font_size"  type="integer" size="4" value="10"   label="Annotation legend font size "/>
 	    	<param name="abundance_threshold"  type="float"   value="20.0"   label="Abundance threshold: minimun abundace value for a clade to be annotated"/>
+	    	<param name="most_abundant"  type="integer" size="4" value="0"   label=" When only lefse_input is provided, you can specify how many clades to highlight "/>
 
-
+   least_biomarkers
     </inputs>
 	<outputs>
             <data  name="output_annot_file"  format="circl"  />
@@ -73,8 +77,8 @@
 
  * **Output of LEfSe**: This file is the result of LEfSe execute on the *Result of MetaPhlAn or HUMAnN analysis* file. This file allow GraPhlAn to highlight for you the found biomarkers.
 
-Input parameters6666
---------------------
+Input parameters
+----------------
  
     --annotations ANNOTATIONS
                         List which levels should be annotated in the tree. Use
@@ -145,7 +149,7 @@
                         the internal nodes
 
     input parameters:
-    You need to provide at least  LEfSe input data 
+
     -i LEFSE_INPUT, --lefse_input LEFSE_INPUT 
                    
     -o LEFSE_OUTPUT, --lefse_output LEFSE_OUTPUT