# HG changeset patch
# User george-weingart
# Date 1410031220 14400
# Node ID c4fd494f5fa55f6ebc973a2c16cc2181d22fd601
# Parent  e0ab17903d9db3ac5b70972d67fc1d968de1860a
Uploaded

diff -r e0ab17903d9d -r c4fd494f5fa5 import2graphlan.xml
--- a/import2graphlan.xml	Sat Sep 06 15:15:42 2014 -0400
+++ b/import2graphlan.xml	Sat Sep 06 15:20:20 2014 -0400
@@ -107,23 +107,34 @@
 
  * **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 parameters1234
-====================
- 
-    **--annotations** ANNOTATIONS List which levels should be annotated in the tree. Use a comma separate values form, e.g., -annotation_levels 1,2,3. Default is None 
- 
+Input parameters
+================
  
+    **--annotations** ANNOTATIONS List which levels should be annotated in the tree. Use a comma separate values form, e.g., -annotation_levels 1,2,3. Default is None
+
+
+
+
     **--external_annotations** EXTERNAL_ANNOTATIONS
-                        List which levels should use the external legend for the annotation. Use a comma separate values form, e.g., --annotation_levels 1,2,3. Default is None 
- 
- 
+                        List which levels should use the external legend for the annotation. Use a comma separate values form,
+                        e.g., --annotation_levels 1,2,3. Default is None
+
+
+
+
     **--background_levels** BACKGROUND_LEVELS
-                        List which levels should be highlight with a shaded background. Use a comma separate values form, e.g.,--background_levels 1,2,3<br><br>
+                        List which levels should be highlight with a shaded
+                        background. Use a comma separate values form, e.g.,
+                        --background_levels 1,2,3
 
 
     **--background_clades** BACKGROUND_CLADES
                         Specify the clades that should be highlight with a  shaded background. Use a comma separate values form and surround the string with " if it contains spaces.
-			Example: --background_clades "Bacteria.Actinobacteria, Bacteria.Bacteroidetes.Bacteroidia,Bacteria.Firmicutes.Clostridia.Clostridiales"
+                        Example: --background_clades "Bacteria.Actinobacteria,
+                        Bacteria.Bacteroidetes.Bacteroidia,
+                        Bacteria.Firmicutes.Clostridia.Clostridiales"
+
+
 
 
     **--background_colors** BACKGROUND_COLORS
@@ -132,6 +143,9 @@
 			Example:  #29cc36, (150; 100; 100), (280;80; 88)
 
 
+
+
+
     **--title TITLE**   If specified set the title of the GraPhlAn plot.
                         Surround the string with " if it contains spaces, e.g., --title "Title example"
 
@@ -149,6 +163,7 @@
                         Default is 20
 
 
+
     **--max_clade_size** MAX_CLADE_SIZE
                         Set the maximum value of clades that are biomarkers.
                         Default is 200
@@ -158,10 +173,14 @@
                         Set a default font size. Default is 10
 
 
+
+
     **--min_font_size** MIN_FONT_SIZE
                         Set the minimum font size to use. Default is 8
 
 
+
+
     **--max_font_size** MAX_FONT_SIZE
                         Set the maximum font size. Default is 12
 
@@ -170,21 +189,28 @@
                         Set the font size for the annotation legend. Default is 10
 
 
+
+
     **--abundance_threshold**  ABUNDANCE_THRESHOLD
                         Set the minimun abundace value for a clade to be annotated. Default is 20.0
 
 
+
+
     **--most_abundant**  MOST_ABUNDANT
                         When only lefse_input is provided, you can specify how many clades highlight. 
 			Since the biomarkers are missing, they will be chosen from the most abundant
 
 
 
+
+
     **--least_biomarkers**  LEAST_BIOMARKERS
                         When only lefse_input is provided, you can specify the 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 discarded from the taxonmy. 
 			Default behavior keep OTU ids in taxonomy
 
@@ -235,3 +261,4 @@
 .. _here:  https://bitbucket.org/nsegata/graphlan/wiki/export2graphlan%20-%20tutorial
   </help>
 </tool>
+