# HG changeset patch
# User george-weingart
# Date 1410025273 14400
# Node ID 34a1b347e2e7c501727fe60c6bad178ccf1c1c8c
# Parent  4dc6abc28ba7a14e18c713cdd4ab040f7cf7b86e
Uploaded

diff -r 4dc6abc28ba7 -r 34a1b347e2e7 import2graphlan.xml
--- a/import2graphlan.xml	Sat Sep 06 13:34:38 2014 -0400
+++ b/import2graphlan.xml	Sat Sep 06 13:41:13 2014 -0400
@@ -78,8 +78,8 @@
 			    	<param name="most_abundant"  type="integer" size="4" value="0"   label=" When only lefse_input is provided, you can specify how many clades to highlight "/>
 				<param name="least_biomarkers"  type="integer" size="4" value="0"   label="Minimum number of biomarkers to extract  "/>
 				<param name="discard_otus" type="select" label="If specified the OTU ids will be discarded from the taxonomy" value="0" >
-						<option value="0">Yes</option>
-						<option value="1">No</option>
+						<option value="0">No</option>
+						<option value="1">Yes</option>
 				</param>
 
     
@@ -109,11 +109,10 @@
  * **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 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,
@@ -179,31 +178,30 @@
                         the internal nodes
  
   
-    Input data matrix parameters:
+Input data matrix parameters
+============================
 
     --sep SEP
+
     --out_table OUT_TABLE   : This is where to write the  processed data matrix to file
 
     --fname_row FNAME_ROW   :  Row number containing the names of the features (default 0, specify -1 if no names are present in the matrix)
 
-    --sname_row SNAME_ROW
-                        column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)
-    --metadata_rows METADATA_ROWS
-                        Row numbers to use as metadata[default None, meaning
-                        no metadata
-    --skip_rows SKIP_ROWS
-                        Row numbers to skip (0-indexed, comma separated) from
-                        the input file[default None, meaning no rows skipped
-    --sperc SPERC         Percentile of sample value distribution for sample
-                        selection
-    --fperc FPERC         Percentile of feature value distribution for sample
-                        selection
-    --stop STOP           Number of top samples to select (ordering based on
-                        percentile specified by --sperc)
-    --ftop FTOP           Number of top features to select (ordering based on
-                        percentile specified by --fperc)
-    --def_na DEF_NA       Set the default value for missing values [default None
-                        which means no replacement]
+    --sname_row SNAME_ROW     column number containing the names of the samples (default 0, specify -1 if no names are present in the matrix)
+
+    --metadata_rows METADATA_ROWS   Row numbers to use as metadata[default None, meaning no metadata
+
+    --skip_rows SKIP_ROWS  Row numbers to skip (0-indexed, comma separated) from the input file[default None, meaning no rows skipped 
+
+    --sperc SPERC         Percentile of sample value distribution for sample selection
+
+    --fperc FPERC         Percentile of feature value distribution for sample selection
+
+    --stop STOP           Number of top samples to select (ordering based on percentile specified by --sperc)
+
+    --ftop FTOP           Number of top features to select (ordering based on percentile specified by --fperc)
+
+    --def_na DEF_NA       Set the default value for missing values [default None which means no replacement]
 
 Integration
 ===========