diff tools/blast_rbh/blast_rbh.xml @ 2:8aa6385b9a05 draft

Uploaded v0.1.0b, more verbose output

--- a/tools/blast_rbh/blast_rbh.xml	Thu May 15 13:11:03 2014 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Fri May 16 08:54:35 2014 -0400
@@ -119,21 +119,28 @@
     <help>
 **What it does**
 
-Takes two FASTA files (species *A* and species *B*), builds a BLAST database
+Takes two FASTA files (*species A* and *species B*), builds a BLAST database
 for each, runs reciprocal BLAST searchs (*A vs B*, and *B vs A*), optionally
-filters these, and then compiles a list of the reciprocal best hits (RBH).
+filters the HSPs, and then compiles a list of the reciprocal best hits (RBH).
 
-The output from this tool is a tabular file containing four columns, with
-the order taken from input file A:
+The output from this tool is a tabular file containing eight columns, with
+information about the BLAST matches used:
 
-====== ======================
+====== =================================
 Column Description
------- ----------------------
-     1 ID from species *A*
-     2 ID from species *B*
+------ ---------------------------------
+     1 ID from *species A*
+     2 ID from *species B*
      3 Bitscore from *A vs B*
-     4 Bitscore from *B vs A*
-====== ======================
+     4 Percentage identity from *A vs B*
+     5 Query coverage from *A vs B*
+     6 Bitscore from *B vs A*
+     7 Percentage identity from *B vs A*
+     8 Query coverage from *B vs A*
+====== =================================
+
+These values correspond to the ``bitscore``, ``pident`` and ``qcovhsp``
+values in the BLAST+ tabular output.
 
 .. class:: warningmark