# HG changeset patch
# User george-weingart
# Date 1410024747 14400
# Node ID c4ffb0c51836e71a5cabc0ab8a9500ad7c28a1a9
# Parent  c670bf87b7332014e699d7d0fbaf4878e7e4dea6
Uploaded

diff -r c670bf87b733 -r c4ffb0c51836 import2graphlan.xml
--- a/import2graphlan.xml	Sat Sep 06 13:22:48 2014 -0400
+++ b/import2graphlan.xml	Sat Sep 06 13:32:27 2014 -0400
@@ -26,6 +26,8 @@
 		#end if
 
 
+
+
 		--title_font_size  $gchoice.title_font_size 
 		--def_clade_size  $gchoice.def_clade_size 
 		--min_clade_size  $gchoice.min_clade_size 
@@ -35,7 +37,11 @@
 		--max_font_size  $gchoice.max_font_size 
 		--annotation_legend_font_size $gchoice.annotation_legend_font_size
 		--abundance_threshold $gchoice.abundance_threshold
-		--least_biomarkers $gchoice.least_biomarkers 	 
+		--least_biomarkers $gchoice.least_biomarkers 
+
+		#if $str($gchoice.discard_otus )  == "1":
+		       	  --discard_otus 
+		#end if	 
 	#end if
 
 	
@@ -71,6 +77,13 @@
 			    	<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 "/>
 				<param name="least_biomarkers"  type="integer" size="4" value="0"   label="Minimum number of biomarkers to extract  "/>
+				<param name="discard_otus" type="select" label="If specified the OTU ids will be discarded from the taxonomy" value="0" >
+						<option value="0">Yes</option>
+						<option value="1">No</option>
+				</param>
+
+    
+
 			</when>
 		 </conditional>
     </inputs>
@@ -87,7 +100,7 @@
 The aim of this tool is to support biologists, helping them by provide the tree and the annotation file for GraPhlAn, automatically.
 
 Input files
------------
+===========
 
 As shown in the image below, export2graphlan can work with just one of the following files or with both of them.
 
@@ -96,7 +109,7 @@
  * **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 parameters
-----------------
+================
  
     --annotations ANNOTATIONS
                         List which levels should be annotated in the tree. Use
@@ -160,20 +173,16 @@
                         minimum number of biomarkers to extract. The taxonomy
                         is parsed, and the level is choosen in order to have
                         at least the specified number of biomarkers
-    --discard_otus        If specified the OTU ids will be discarde from the
+    --discard_otus      If specified the OTU ids will be discarded from the
                         taxonmy. Default behavior keep OTU ids in taxonomy
-    --internal_levels     If specified sum-up from leaf to root the abundances
+    --internal_levels   If specified sum-up from leaf to root the abundances
                         values. Default behavior do not sum-up abundances on
                         the internal nodes
  
-
-    output parameters:
-
-    -t TREE, --tree TREE  Output filename where save the input tree for GraPhlAn
-
-    -a ANNOTATION, --annotation ANNOTATION :  This is the Output filename where to save GraPhlAn annotation
   
     Input data matrix parameters:
+    =============================
+
     --sep SEP
     --out_table OUT_TABLE   : This is where to write the  processed data matrix to file