changeset 46:6c8594d2f7e2 draft

Uploaded

--- a/import2graphlan.xml	Sat Sep 06 14:02:24 2014 -0400
+++ b/import2graphlan.xml	Sat Sep 06 14:05:09 2014 -0400
@@ -112,35 +112,44 @@
  
     **--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
 
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     **--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
 
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     **--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
 
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     **--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"
 
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     **--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:  #29cc36, (150; 100; 100), (280;80; 88)
 
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     **--title TITLE**   If specified set the title of the GraPhlAn plot.
                         Surround the string with " if it contains spaces, e.g., --title "Title example"
 
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     **--title_font_size** TITLE_FONT_SIZE
                         Set the title font size. Default is 15
 
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     **--def_clade_size** DEF_CLADE_SIZE
                         Set a default size for clades that are not found as biomarkers by LEfSe. Default is 10
 
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     **--min_clade_size** MIN_CLADE_SIZE
                         Set the minimum value of clades that are biomarkers.
                         Default is 20
@@ -149,32 +158,42 @@
                         Set the maximum value of clades that are biomarkers.
                         Default is 200
 
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     **--def_font_size**  DEF_FONT_SIZE
                         Set a default font size. Default is 10
 
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     **--min_font_size** MIN_FONT_SIZE
                         Set the minimum font size to use. Default is 8
 
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     **--max_font_size** MAX_FONT_SIZE
                         Set the maximum font size. Default is 12
 
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     **--annotation_legend_font_size**  ANNOTATION_LEGEND_FONT_SIZE
                         Set the font size for the annotation legend. Default is 10
 
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     **--abundance_threshold**  ABUNDANCE_THRESHOLD
                         Set the minimun abundace value for a clade to be annotated. Default is 20.0
 
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     **--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
 
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     **--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
 
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     **--discard_otus**     If specified the OTU ids will be discarded from the taxonmy. 
 			Default behavior keep OTU ids in taxonomy
 
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     **--internal_levels**   If specified sum-up from leaf to root the abundances values. Default behavior do not sum-up abundances on the internal nodes