diff tools/blast_rbh/blast_rbh.xml @ 6:e47960bcdccb draft

Uploaded v0.1.0f, exclude tied best hits

--- a/tools/blast_rbh/blast_rbh.xml	Tue May 20 06:33:08 2014 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Wed May 21 06:33:50 2014 -0400
@@ -125,6 +125,25 @@
             <param name="q_cover" value="0.0"/>
             <output name="output" file="rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular" ftype="tabular"/>
         </test>
+        <!-- this pair of examples test tied best hits -->	
+        <test>
+            <param name="fasta_a" value="k12_ten_proteins.fasta" ftype="fasta"/>
+            <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/>
+            <param name="dbtype" value="nprot"/>
+            <param name="nucl_type" value="blastp"/>
+            <param name="identity" value="0.0"/>
+            <param name="q_cover" value="0.0"/>
+            <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/>
+        </test>
+        <test>
+            <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/>
+            <param name="fasta_b" value="k12_ten_proteins.fasta" ftype="fasta"/>
+            <param name="dbtype" value="nprot"/>
+            <param name="nucl_type" value="blastp"/>
+            <param name="identity" value="0.0"/>
+            <param name="q_cover" value="0.0"/>
+            <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/>
+        </test>
     </tests>
     <help>
 **What it does**
@@ -159,6 +178,11 @@
 The coverage values are given by the HSP alignment length divided by the
 sequence length (adjusted by a factor of three for TBLASTX).
 
+Note that if a sequence has equally scoring top BLAST matches to multiple
+sequence in the other file, it will not be considered for an RBH. This
+can happen following gene duplication, or for (near) identical gene
+duplicates.
+
 .. class:: warningmark
 
 **Note**