Mercurial > repos > george-weingart > graphlan_import

changeset 59:000d65b33ecd draft

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Uploaded
author george-weingart
date Sat, 06 Sep 2014 15:38:54 -0400
parents 3712843df8d7
children 39126c375dd4
files import2graphlan.xml
diffstat 1 files changed, 11 insertions(+), 40 deletions(-) [+]
line wrap: on
line diff
--- a/import2graphlan.xml	Sat Sep 06 15:35:00 2014 -0400
+++ b/import2graphlan.xml	Sat Sep 06 15:38:54 2014 -0400
@@ -138,65 +138,36 @@
     **--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
+    **--min_clade_size** MIN_CLADE_SIZE  Set the minimum value of clades that are biomarkers. Default is 20
 
 
-
-    **--max_clade_size** MAX_CLADE_SIZE
-                        Set the maximum value of clades that are biomarkers.
-                        Default is 200
+    **--max_clade_size** MAX_CLADE_SIZE Set the maximum value of clades that are biomarkers.  Default is 200
 
 
-    **--def_font_size**  DEF_FONT_SIZE
-                        Set a default font size. Default is 10
-
-
+    **--def_font_size**  DEF_FONT_SIZE  Set a default font size. Default is 10
 
 
-    **--min_font_size** MIN_FONT_SIZE
-                        Set the minimum font size to use. Default is 8
+    **--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
+    **--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
+    **--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
 
 
-
-    **--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
 
 
-    **--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
 
 
-    **--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
-
+    **--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
 ============================