changeset 43:c5c1037078e5 draft

Uploaded

--- a/import2graphlan.xml	Sat Sep 06 13:45:33 2014 -0400
+++ b/import2graphlan.xml	Sat Sep 06 13:51:49 2014 -0400
@@ -115,70 +115,72 @@
 
     **--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
+    **--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
+    **--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"
 
-    --background_colors BACKGROUND_COLORS
+    **--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:
-                        --background_colors "#29cc36, (150; 100; 100), (280;
-                        80; 88)"
+			--------
+                        --background_colors "#29cc36, (150; 100; 100), (280;80; 88)"
 
-    --title TITLE         If specified set the title of the GraPhlAn plot.
-
+    **--title TITLE**   If specified set the title of the GraPhlAn plot.
                         Surround the string with " if it contains spaces, e.g., --title "Title example"
 
-    --title_font_size TITLE_FONT_SIZE
+    **--title_font_size** TITLE_FONT_SIZE
                         Set the title font size. Default is 15
-    --def_clade_size DEF_CLADE_SIZE
-                        Set a default size for clades that are not found as
-                        biomarkers by LEfSe. Default is 10
-    --min_clade_size MIN_CLADE_SIZE
+
+    **--def_clade_size** DEF_CLADE_SIZE
+                        Set a default size for clades that are not found as biomarkers by LEfSe. Default is 10
+
+    **--min_clade_size** MIN_CLADE_SIZE
                         Set the minimum value of clades that are biomarkers.
                         Default is 20
-    --max_clade_size MAX_CLADE_SIZE
+
+    **--max_clade_size** MAX_CLADE_SIZE
                         Set the maximum value of clades that are biomarkers.
                         Default is 200
-    --def_font_size DEF_FONT_SIZE
+
+    **--def_font_size**  DEF_FONT_SIZE
                         Set a default font size. Default is 10
-    --min_font_size MIN_FONT_SIZE
+
+    **--min_font_size** MIN_FONT_SIZE
                         Set the minimum font size to use. Default is 8
-    --max_font_size MAX_FONT_SIZE
+
+    **--max_font_size** MAX_FONT_SIZE
                         Set the maximum font size. Default is 12
-    --annotation_legend_font_size ANNOTATION_LEGEND_FONT_SIZE
-                        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
-    --internal_levels   If specified sum-up from leaf to root the abundances
-                        values. Default behavior do not sum-up abundances on
-                        the internal nodes
+
+    **--annotation_legend**_font_size ANNOTATION_LEGEND_FONT_SIZE
+                        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
+
+    **--internal_levels**   If specified sum-up from leaf to root the abundances values. Default behavior do not sum-up abundances on the internal nodes
  
   
 Input data matrix parameters