changeset 42:fa2bd894219f draft

Uploaded

--- a/import2graphlan.xml	Sat Sep 06 13:41:13 2014 -0400
+++ b/import2graphlan.xml	Sat Sep 06 13:45:33 2014 -0400
@@ -111,34 +111,37 @@
 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
+    **--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,
+    **--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
+
     --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
+
     --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.
+                        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"
+
     --background_colors BACKGROUND_COLORS
-                        Set the color to use for the shaded background. Colors
-                        can be either in RGB or HSV (using a semi-colon to
-                        separate values, surrounded with ()) format. Use a
-                        comma separate values form and surround the string
-                        with " if it contains spaces. Example:
+                        Set the color to use for the shaded background. Colors can be either in RGB or HSV (using a semi-colon to separate values, surrounded with ()) format. 
+			
+			Use a comma separate values form and surround the string with " if it contains spaces. 
+			
+			Example:
                         --background_colors "#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"
+
+                        Surround the string with " if it contains spaces, e.g., --title "Title example"
+
     --title_font_size TITLE_FONT_SIZE
                         Set the title font size. Default is 15
     --def_clade_size DEF_CLADE_SIZE