# HG changeset patch
# User george-weingart
# Date 1409860356 14400
# Node ID 51466b550e7779e95a3487d0d081596e687ebe47
# Parent  33a3a37c7872f32a322669ff0cf4ab89e06356bb
Uploaded

diff -r 33a3a37c7872 -r 51466b550e77 export2graphlan.xml
--- a/export2graphlan.xml	Thu Sep 04 15:35:20 2014 -0400
+++ b/export2graphlan.xml	Thu Sep 04 15:52:36 2014 -0400
@@ -6,27 +6,39 @@
 	-o $out_data
 	-t $output_tree_file 
 	-a $output_annot_file 
-	--title $export_title
+
 	--annotations $export_annotations 
 	--external_annotations $export_external_annotations
 	--background_levels  $background_levels 
 	#if $str($background_clades)  != " ":
                	--background_clades  $background_clades
 	#end if
-
-
+	#if $str($background_colors)  != " ":
+               	--background_colors  $background_colors
+	#end if
+	#if $str($export_title)  != " ":
+               	--title $export_title
+	#end if
+	--title_font_size  $title_font_size 
+	--def_clade_size  $def_clade_size 
+	--min_clade_size  $min_clade_size 
+	--max_clade_size  $max_clade_size 
 	--skip_rows 1,2 
    </command>
    
 	<inputs>
 		<param format="tabular" name="inp_data" type="data" label="Input used to run Lefse -  See samples below - Please use Galaxy Get-Data/Upload-File. Use File-Type = Tabular" 	help="This is the file that was used as input for Lefse"/>
 		<param format="lefse_res" name="out_data" type="data" label="Output of  Lefse"  help="This is the  Lefse output file"/>	
-	    	<param name="export_title" type="text" format="text" label="Title" value="Title"/>
 	   	 <param name="export_annotations" type="text" format="text" label="Annotations" value="2,3"/>
 	   	 <param name="export_external_annotations" type="text" format="text" label="External Annotations" value="4,5,6"/>   
 		<param name="background_levels" type="text" format="text" label="Background Levels" value="1,2,3"/>   
 		<param name="background_clades" type="text" format="text" label="Background Clades" value=" " />  
-
+		<param name="background_colors" type="text" format="text" label="Background Colors" value=" " />  
+	    	<param name="export_title" type="text" format="text" label="Title" value=" "/>
+	    	<param name="title_font_size"  type="integer" size="4" value="15"   label="Title font size"/>
+	    	<param name="def_clade_size"  type="integer" size="4" value="0"   label="Default Clade size"/>
+	    	<param name="min_clade_size"  type="integer" size="4" value="20"   label="Minimum Clade size that are Biomarkers"/>
+	    	<param name="max_clade_size"  type="integer" size="4" value="200"   label="Maximum Clade size that are Biomarkers"/>
 
     </inputs>
 	<outputs>
@@ -50,7 +62,7 @@
 
  * **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 parameters5555
+Input parameters6666
 --------------------
  
     --annotations ANNOTATIONS