changeset 14:40c85a67e645 draft

Uploaded v0.1.6, offer the new blastp-fast tasked added in BLAST+ 2.2.30.

--- a/tools/blast_rbh/README.rst	Thu Oct 30 14:20:48 2014 -0400
+++ b/tools/blast_rbh/README.rst	Thu Nov 27 11:41:08 2014 -0500
@@ -62,6 +62,7 @@
           not treating this as an error, leading to confusing RBH output).
 v0.1.5  - Clarify documentation for using the Python script outside Galaxy.
         - Updated to depend on NCBI BLAST+ 2.2.30 via ToolShed install.
+v0.1.6  - Offer the new blastp-fast tasked added in BLAST+ 2.2.30.
 ======= ======================================================================
 
 

--- a/tools/blast_rbh/blast_rbh.py	Thu Oct 30 14:20:48 2014 -0400
+++ b/tools/blast_rbh/blast_rbh.py	Thu Nov 27 11:41:08 2014 -0500
@@ -32,7 +32,7 @@
 
 if "--version" in sys.argv[1:]:
     #TODO - Capture version of BLAST+ binaries too?
-    print "BLAST RBH v0.1.5"
+    print "BLAST RBH v0.1.6"
     sys.exit(0)
 
 #Parse Command Line
@@ -107,7 +107,7 @@
     else:
         stop_err("Invalid BLAST type for BLASTN: %r" % blast_type)
 elif dbtype == "prot":
-    if blast_type not in ["blastp", "blastp-short"]:
+    if blast_type not in ["blastp", "blastp-fast", "blastp-short"]:
         stop_err("Invalid BLAST type for BLASTP: %r" % blast_type)
     blast_cmd = "blastp -task %s" % blast_type
 else:
@@ -329,7 +329,7 @@
 outfile.close()
 print "Done, %i RBH found" % count
 if tie_warning:
-    sys.stderr.write("Warning: Sequencies with tied best hits found, you may have duplicates/clusters\n")
+    sys.stderr.write("Warning: Sequences with tied best hits found, you may have duplicates/clusters\n")
 
 #Remove temp files...
 shutil.rmtree(base_path)

--- a/tools/blast_rbh/blast_rbh.xml	Thu Oct 30 14:20:48 2014 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Thu Nov 27 11:41:08 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.5">
+<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.6">
     <description>from two FASTA files</description>
     <requirements>
         <requirement type="package" version="1.64">biopython</requirement>
@@ -45,6 +45,7 @@
             <when value="prot">
                 <param name="prot_type" type="select" display="radio" label="Type of BLAST">
                     <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option>
+                    <option value="blastp-fast">blastp-fast - Uses longer words as described by Shiryev et al (2007)</option>
                     <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option>
                 </param>
             </when>
@@ -163,7 +164,7 @@
             <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/>
             <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/>
             <param name="dbtype" value="prot"/>
-            <param name="nucl_type" value="blastp"/>
+            <param name="nucl_type" value="blastp-fast"/>
             <param name="identity" value="80.0"/>
             <param name="q_cover" value="80.0"/>
             <output name="output" file="rbh_blastp_k12_self.tabular" ftype="tabular"/>