# HG changeset patch
# User peterjc
# Date 1670342016 0
# Node ID 8f4500f6f2aae46b6f37835d3e104c76cac8d598
# Parent  d8d9a906958665b88f0bc2ac65ed9e70b6704fe8
Refactored to use more than one Python file (internal change only).

diff -r d8d9a9069586 -r 8f4500f6f2aa tools/blast_rbh/README.rst
--- a/tools/blast_rbh/README.rst	Wed Apr 19 07:44:47 2017 -0400
+++ b/tools/blast_rbh/README.rst	Tue Dec 06 15:53:36 2022 +0000
@@ -24,13 +24,13 @@
 NCBI BLAST+ integrated into Galaxy.
 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo
 *GigaScience* 2015, 4:39
-DOI: http://dx.doi.org/10.1186/s13742-015-0080-7
+https://doi.org/10.1186/s13742-015-0080-7
 
 You should also cite the NCBI BLAST+ tools:
 
 BLAST+: architecture and applications.
 C. Camacho et al. *BMC Bioinformatics* 2009, 10:421.
-DOI: http://dx.doi.org/10.1186/1471-2105-10-421
+https://doi.org/10.1186/1471-2105-10-421
 
 
 Automated Installation
@@ -43,9 +43,10 @@
 Manual Installation
 ===================
 
-There are just two files to install:
+There are just three files to install:
 
 - ``blast_rbh.py`` (the Python script)
+- ``best_hits.py`` (helper script, put in same directory)
 - ``blast_rbh.xml`` (the Galaxy tool definition)
 
 The suggested location is in a ``tools/blast_rbh/`` folder. You will then
@@ -91,6 +92,9 @@
 v0.1.11 - Updated to depend on NCBI BLAST+ 2.5.0 via ToolShed or BioConda.
         - Update Biopython dependency.
         - Tweak Python script to work under Python 2 or Python 3.
+v0.1.12 - Use ``<command detect_errors="aggressive">`` (internal change only).
+        - Single quote command line arguments (internal change only).
+v0.2.0  - Refactored to use more than one Python file (internal change only).
 ======= ======================================================================
 
 
@@ -116,7 +120,7 @@
 
     $ planemo shed_upload --tar_only tools/blast_rbh/
     ...
-    $ tar -tzf shed_upload.tar.gz 
+    $ tar -tzf shed_upload.tar.gz
     test-data/four_human_proteins.fasta
     test-data/k12_edited_proteins.fasta
     test-data/k12_ten_proteins.fasta
diff -r d8d9a9069586 -r 8f4500f6f2aa tools/blast_rbh/best_hits.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/blast_rbh/best_hits.py	Tue Dec 06 15:53:36 2022 +0000
@@ -0,0 +1,124 @@
+#!/usr/bin/env python
+"""Helper code for BLAST Reciprocal Best Hit (RBH) from two BLAST tabular files.
+
+This module defines a function best_hits to return the best hit in a BLAST
+tabular file, intended for use in finding BLAST Reciprocal Best Hits (RBH).
+
+The code in this module originated from blast_rbh.py in
+https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh
+
+Please cite the author per instructions in
+https://github.com/peterjc/galaxy_blast/blob/master/tools/blast_rbh/README.rst
+"""
+
+import sys
+
+tie_warning = 0
+
+c_query = 0
+c_match = 1
+c_score = 2
+c_identity = 3
+c_coverage = 4
+c_qlen = 5
+c_length = 6
+
+cols = "qseqid sseqid bitscore pident qcovhsp qlen length"
+
+
+def best_hits(blast_tabular, min_identity=70, min_coverage=50, ignore_self=False):
+    """Parse BLAST tabular output returning the best hit.
+
+    Argument blast_tabular should be a filename, containing BLAST tabular
+    output with "qseqid sseqid bitscore pident qcovhsp qlen length" as
+    the columns.
+
+    Parses the tabular file, iterating over the results as 2-tuples
+    of (query name, tuple of values for the best hit).
+
+    One hit is returned for tied best hits to the same sequence
+    (e.g. repeated domains).
+
+    Tied best hits to different sequences are NOT returned. Instead,
+    global variable tie_warning is incremented.
+    """
+    global tie_warning
+    current = None
+    best_score = None
+    best = None
+    col_count = len(cols.split())
+    with open(blast_tabular) as h:
+        for line in h:
+            if line.startswith("#"):
+                continue
+            parts = line.rstrip("\n").split("\t")
+            if len(parts) != col_count:
+                # Using NCBI BLAST+ 2.2.27 the undefined field is ignored
+                # Even NCBI BLAST+ 2.5.0 silently ignores unknown fields :(
+                sys.exit(
+                    "Old version of NCBI BLAST? Expected %i columns, got %i:\n%s\n"
+                    "Note the qcovhsp field was only added in version 2.2.28\n"
+                    % (col_count, len(parts), line)
+                )
+            if (
+                float(parts[c_identity]) < min_identity
+                or float(parts[c_coverage]) < min_coverage
+            ):
+                continue
+            a = parts[c_query]
+            b = parts[c_match]
+            if ignore_self and a == b:
+                continue
+            score = float(parts[c_score])
+            qlen = int(parts[c_qlen])
+            length = int(parts[c_length])
+            # print("Considering hit for %s to %s with score %s..." % (a, b, score))
+            if current is None:
+                # First hit
+                assert best is None
+                assert best_score is None
+                best = dict()
+                # Now append this hit...
+            elif a != current:
+                # New hit
+                if len(best) == 1:
+                    # Unambiguous (no tied matches)
+                    yield current, list(best.values())[0]
+                else:
+                    # print("%s has %i equally good hits: %s"
+                    #       % (a, len(best), ", ".join(best)))
+                    tie_warning += 1
+                best = dict()
+                # Now append this hit...
+            elif score < best_score:
+                # print("No improvement for %s, %s < %s" % (a, score, best_score))
+                continue
+            elif score > best_score:
+                # This is better, discard old best
+                best = dict()
+                # Now append this hit...
+            else:
+                # print("Tied best hits for %s" % a)
+                assert best_score == score
+                # Now append this hit...
+            current = a
+            best_score = score
+            # This will collapse two equally good hits
+            # to the same target (e.g. duplicated domain)
+            best[b] = (
+                b,
+                score,
+                parts[c_score],
+                parts[c_identity],
+                parts[c_coverage],
+                qlen,
+                length,
+            )
+    # Best hit for final query, if unambiguous:
+    if current is not None:
+        if len(best) == 1:
+            yield current, list(best.values())[0]
+        else:
+            # print("%s has %i equally good hits: %s"
+            # % (a, len(best), ", ".join(best)))
+            tie_warning += 1
diff -r d8d9a9069586 -r 8f4500f6f2aa tools/blast_rbh/blast_rbh.py
--- a/tools/blast_rbh/blast_rbh.py	Wed Apr 19 07:44:47 2017 -0400
+++ b/tools/blast_rbh/blast_rbh.py	Tue Dec 06 15:53:36 2022 +0000
@@ -24,11 +24,14 @@
 import shutil
 import sys
 import tempfile
+import best_hits
+
 
 from optparse import OptionParser
 
 
 def run(cmd):
+    """Run the given command line string."""
     return_code = os.system(cmd)
     if return_code:
         sys.exit("Error %i from: %s" % (return_code, cmd))
@@ -36,7 +39,7 @@
 
 if "--version" in sys.argv[1:]:
     # TODO - Capture version of BLAST+ binaries too?
-    print("BLAST RBH v0.1.11")
+    print("BLAST RBH v0.2.0")
     sys.exit(0)
 
 try:
@@ -54,33 +57,62 @@
 
 $ python blast_rbh.py -a prot -t blasp -o output.tsv protA.fasta protB.fasta
 
-There is additional guideance in the help text in the blast_rbh.xml file,
+There is additional guidance in the help text in the blast_rbh.xml file,
 which is shown to the user via the Galaxy interface to this tool.
 """
 
 parser = OptionParser(usage=usage)
-parser.add_option("-a", "--alphabet", dest="dbtype",
-                  default=None,
-                  help="Alphabet type (nucl or prot; required)")
-parser.add_option("-t", "--task", dest="task",
-                  default=None,
-                  help="BLAST task (e.g. blastp, blastn, megablast; required)")
-parser.add_option("-i", "--identity", dest="min_identity",
-                  default="70",
-                  help="Minimum percentage identity (optional, default 70)")
-parser.add_option("-c", "--coverage", dest="min_coverage",
-                  default="50",
-                  help="Minimum HSP coverage (optional, default 50)")
-parser.add_option("--nr", dest="nr", default=False, action="store_true",
-                  help="Preprocess FASTA files to collapse identitical "
-                  "entries (make sequences non-redundant)")
-parser.add_option("-o", "--output", dest="output",
-                  default=None, metavar="FILE",
-                  help="Output filename (required)")
-parser.add_option("--threads", dest="threads",
-                  default=threads,
-                  help="Number of threads when running BLAST. Defaults to the "
-                       "$GALAXY_SLOTS environment variable if set, or 1.")
+parser.add_option(
+    "-a",
+    "--alphabet",
+    dest="dbtype",
+    default=None,
+    help="Alphabet type (nucl or prot; required)",
+)
+parser.add_option(
+    "-t",
+    "--task",
+    dest="task",
+    default=None,
+    help="BLAST task (e.g. blastp, blastn, megablast; required)",
+)
+parser.add_option(
+    "-i",
+    "--identity",
+    dest="min_identity",
+    default="70",
+    help="Minimum percentage identity (optional, default 70)",
+)
+parser.add_option(
+    "-c",
+    "--coverage",
+    dest="min_coverage",
+    default="50",
+    help="Minimum HSP coverage (optional, default 50)",
+)
+parser.add_option(
+    "--nr",
+    dest="nr",
+    default=False,
+    action="store_true",
+    help="Preprocess FASTA files to collapse identitical "
+    "entries (make sequences non-redundant)",
+)
+parser.add_option(
+    "-o",
+    "--output",
+    dest="output",
+    default=None,
+    metavar="FILE",
+    help="Output filename (required)",
+)
+parser.add_option(
+    "--threads",
+    dest="threads",
+    default=threads,
+    help="Number of threads when running BLAST. Defaults to the "
+    "$GALAXY_SLOTS environment variable if set, or 1.",
+)
 options, args = parser.parse_args()
 
 if len(args) != 2:
@@ -103,13 +135,17 @@
 try:
     min_identity = float(options.min_identity)
 except ValueError:
-    sys.exit("Expected number between 0 and 100 for minimum identity, not %r" % min_identity)
+    sys.exit(
+        "Expected number between 0 and 100 for minimum identity, not %r" % min_identity
+    )
 if not (0 <= min_identity <= 100):
     sys.exit("Expected minimum identity between 0 and 100, not %0.2f" % min_identity)
 try:
     min_coverage = float(options.min_coverage)
 except ValueError:
-    sys.exit("Expected number between 0 and 100 for minimum coverage, not %r" % min_coverage)
+    sys.exit(
+        "Expected number between 0 and 100 for minimum coverage, not %r" % min_coverage
+    )
 if not (0 <= min_coverage <= 100):
     sys.exit("Expected minimum coverage between 0 and 100, not %0.2f" % min_coverage)
 
@@ -137,7 +173,9 @@
 try:
     threads = int(options.threads)
 except ValueError:
-    sys.exit("Expected positive integer for number of threads, not %r" % options.threads)
+    sys.exit(
+        "Expected positive integer for number of threads, not %r" % options.threads
+    )
 if threads < 1:
     sys.exit("Expected positive integer for number of threads, not %r" % threads)
 
@@ -157,95 +195,9 @@
     b_vs_a = os.path.join(base_path, "B_vs_A.tabular")
 log = os.path.join(base_path, "blast.log")
 
-cols = "qseqid sseqid bitscore pident qcovhsp qlen length"  # Or qcovs?
-c_query = 0
-c_match = 1
-c_score = 2
-c_identity = 3
-c_coverage = 4
-c_qlen = 5
-c_length = 6
-
-tie_warning = 0
-
-
-def best_hits(blast_tabular, ignore_self=False):
-    """Iterate over BLAST tabular output, returns best hits as 2-tuples.
-
-    Each return value is (query name, tuple of value for the best hit).
-
-    Tied best hits to different sequences are NOT returned.
-
-    One hit is returned for tied best hits to the same sequence
-    (e.g. repeated domains).
-    """
-    global tie_warning
-    current = None
-    best_score = None
-    best = None
-    col_count = len(cols.split())
-    with open(blast_tabular) as h:
-        for line in h:
-            if line.startswith("#"):
-                continue
-            parts = line.rstrip("\n").split("\t")
-            if len(parts) != col_count:
-                # Using NCBI BLAST+ 2.2.27 the undefined field is ignored
-                # Even NCBI BLAST+ 2.5.0 silently ignores unknown fields :(
-                sys.exit("Old version of NCBI BLAST? Expected %i columns, got %i:\n%s\n"
-                         "Note the qcovhsp field was only added in version 2.2.28\n"
-                         % (col_count, len(parts), line))
-            if float(parts[c_identity]) < min_identity or float(parts[c_coverage]) < min_coverage:
-                continue
-            a = parts[c_query]
-            b = parts[c_match]
-            if ignore_self and a == b:
-                continue
-            score = float(parts[c_score])
-            qlen = int(parts[c_qlen])
-            length = int(parts[c_length])
-            # print("Considering hit for %s to %s with score %s..." % (a, b, score))
-            if current is None:
-                # First hit
-                assert best is None
-                assert best_score is None
-                best = dict()
-                # Now append this hit...
-            elif a != current:
-                # New hit
-                if len(best) == 1:
-                    # Unambiguous (no tied matches)
-                    yield current, list(best.values())[0]
-                else:
-                    # print("%s has %i equally good hits: %s" % (a, len(best), ", ".join(best)))
-                    tie_warning += 1
-                best = dict()
-                # Now append this hit...
-            elif score < best_score:
-                # print("No improvement for %s, %s < %s" % (a, score, best_score))
-                continue
-            elif score > best_score:
-                # This is better, discard old best
-                best = dict()
-                # Now append this hit...
-            else:
-                # print("Tied best hits for %s" % a)
-                assert best_score == score
-                # Now append this hit...
-            current = a
-            best_score = score
-            # This will collapse two equally good hits to the same target (e.g. duplicated domain)
-            best[b] = (b, score, parts[c_score], parts[c_identity], parts[c_coverage], qlen, length)
-    # Best hit for final query, if unambiguous:
-    if current is not None:
-        if len(best) == 1:
-            yield current, list(best.values())[0]
-        else:
-            # print("%s has %i equally good hits: %s" % (a, len(best), ", ".join(best)))
-            tie_warning += 1
-
 
 def check_duplicate_ids(filename):
+    """Check for duplicate identifiers in a FASTA file."""
     # Copied from tools/ncbi_blast_plus/check_no_duplicates.py
     # TODO - just use Biopython's FASTA parser?
     if not os.path.isfile(filename):
@@ -267,11 +219,12 @@
 
 
 def make_nr(input_fasta, output_fasta, sep=";"):
+    """Make the sequences in a FASTA file non-redundant."""
     # TODO - seq-hash based to avoid loading everything into RAM?
     by_seq = dict()
     try:
         from Bio import SeqIO
-    except KeyError:
+    except ImportError:
         sys.exit("Missing Biopython")
     for record in SeqIO.parse(input_fasta, "fasta"):
         s = str(record.seq).upper()
@@ -300,8 +253,10 @@
                 elif record.id in duplicates:
                     continue
                 SeqIO.write(record, handle, "fasta")
-        print("%i unique entries; removed %i duplicates leaving %i representative records"
-              % (unique, len(duplicates), len(representatives)))
+        print(
+            "%i unique entries; removed %i duplicates leaving %i representative records"
+            % (unique, len(duplicates), len(representatives))
+        )
     else:
         os.symlink(os.path.abspath(input_fasta), output_fasta)
         print("No perfect duplicates in file, %i unique entries" % unique)
@@ -320,31 +275,55 @@
     fasta_b = tmp_b
 
 # TODO - Report log in case of error?
-run('%s -dbtype %s -in "%s" -out "%s" -logfile "%s"' % (makeblastdb_exe, dbtype, fasta_a, db_a, log))
+run(
+    '%s -dbtype %s -in "%s" -out "%s" -logfile "%s"'
+    % (makeblastdb_exe, dbtype, fasta_a, db_a, log)
+)
 if not self_comparison:
-    run('%s -dbtype %s -in "%s" -out "%s" -logfile "%s"' % (makeblastdb_exe, dbtype, fasta_b, db_b, log))
+    run(
+        '%s -dbtype %s -in "%s" -out "%s" -logfile "%s"'
+        % (makeblastdb_exe, dbtype, fasta_b, db_b, log)
+    )
 # print("BLAST databases prepared.")
-run('%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i'
-    % (blast_cmd, fasta_a, db_b, a_vs_b, cols, threads))
+run(
+    '%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i'
+    % (blast_cmd, fasta_a, db_b, a_vs_b, best_hits.cols, threads)
+)
 # print("BLAST species A vs species B done.")
 if not self_comparison:
-    run('%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i'
-        % (blast_cmd, fasta_b, db_a, b_vs_a, cols, threads))
+    run(
+        '%s -query "%s" -db "%s" -out "%s" -outfmt "6 %s" -num_threads %i'
+        % (blast_cmd, fasta_b, db_a, b_vs_a, best_hits.cols, threads)
+    )
     # print("BLAST species B vs species A done.")
 
 
-best_b_vs_a = dict(best_hits(b_vs_a, self_comparison))
+best_b_vs_a = dict(
+    best_hits.best_hits(b_vs_a, min_identity, min_coverage, self_comparison)
+)
 
 
 count = 0
-outfile = open(out_file, 'w')
-outfile.write("#A_id\tB_id\tA_length\tB_length\tA_qcovhsp\tB_qcovhsp\tlength\tpident\tbitscore\n")
-for a, (b, a_score_float, a_score_str,
-        a_identity_str, a_coverage_str, a_qlen, a_length) in best_hits(a_vs_b, self_comparison):
+outfile = open(out_file, "w")
+outfile.write(
+    "#A_id\tB_id\tA_length\tB_length\tA_qcovhsp\tB_qcovhsp\tlength\tpident\tbitscore\n"
+)
+for (
+    a,
+    (b, a_score_float, a_score_str, a_identity_str, a_coverage_str, a_qlen, a_length),
+) in best_hits.best_hits(a_vs_b, min_identity, min_coverage, self_comparison):
     if b not in best_b_vs_a:
         # Match b has no best hit
         continue
-    a2, b_score_float, b_score_str, b_identity_str, b_coverage_str, b_qlen, b_length = best_b_vs_a[b]
+    (
+        a2,
+        b_score_float,
+        b_score_str,
+        b_identity_str,
+        b_coverage_str,
+        b_qlen,
+        b_length,
+    ) = best_b_vs_a[b]
     if a != a2:
         # Not an RBH
         continue
@@ -365,8 +344,11 @@
     count += 1
 outfile.close()
 print("Done, %i RBH found" % count)
-if tie_warning:
-    sys.stderr.write("Warning: Sequences with tied best hits found, you may have duplicates/clusters\n")
+if best_hits.tie_warning:
+    sys.stderr.write(
+        "Warning: Sequences with tied best hits found, "
+        "you may have duplicates/clusters\n"
+    )
 
 # Remove temp files...
 shutil.rmtree(base_path)
diff -r d8d9a9069586 -r 8f4500f6f2aa tools/blast_rbh/blast_rbh.xml
--- a/tools/blast_rbh/blast_rbh.xml	Wed Apr 19 07:44:47 2017 -0400
+++ b/tools/blast_rbh/blast_rbh.xml	Tue Dec 06 15:53:36 2022 +0000
@@ -1,19 +1,14 @@
-<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11">
+<tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.2.0">
     <description>from two FASTA files</description>
     <requirements>
         <requirement type="package" version="1.67">biopython</requirement>
         <requirement type="package" version="2.5.0">blast</requirement>
     </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <version_command interpreter="python">
-blast_rbh.py --version
+    <version_command>
+python $__tool_directory__/blast_rbh.py --version
     </version_command>
-    <command interpreter="python">
-blast_rbh.py "$fasta_a" "$fasta_b"
+    <command detect_errors="aggressive">
+python $__tool_directory__/blast_rbh.py '$fasta_a' '$fasta_b'
 -a $seq.dbtype
 #if $seq.dbtype=="nucl"
 -t $seq.nucl_type
@@ -23,16 +18,16 @@
 $make_nr
 -i $identity
 -c $q_cover
--o "$output"
+-o '$output'
     </command>
     <inputs>
         <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
         <param name="fasta_a" type="data" format="fasta"
-	       label="Genes/proteins from species A"
-	       help="FASTA file, one sequence per gene/protein." /> 
+               label="Genes/proteins from species A"
+               help="FASTA file, one sequence per gene/protein."/>
         <param name="fasta_b" type="data" format="fasta"
-	       label="Genes/proteins from species B"
-	       help="FASTA file, one sequence per gene/protein." /> 
+               label="Genes/proteins from species B"
+               help="FASTA file, one sequence per gene/protein."/>
         <conditional name="seq">
             <param name="dbtype" type="select" label="Molecule type of FASTA inputs">
                 <option value="prot">protein</option>
@@ -55,14 +50,14 @@
                 </param>
             </when>
         </conditional>
-	<param name="identity" type="float" value="70" min="0" max="100"
-	       label="Minimum percentage identity for BLAST matches"
-	       help="Default is 70%, use 0 for no filtering." />
+        <param name="identity" type="float" value="70" min="0" max="100"
+               label="Minimum percentage identity for BLAST matches"
+               help="Default is 70%, use 0 for no filtering." />
         <param name="q_cover" type="float" value="50" min="0" max="100"
-	       label="Minimum percentage query coverage for BLAST matches"
-	       help="Default is 50%, use 0 for no filtering." />
+               label="Minimum percentage query coverage for BLAST matches"
+               help="Default is 50%, use 0 for no filtering." />
         <param name="make_nr" type="boolean" checked="false" truevalue="--nr" falsevalue=""
-	       label="Process input FASTA files to collapse identical sequences"
+               label="Process input FASTA files to collapse identical sequences"
                help="i.e. First make the input non-redundant" />
     </inputs>
     <outputs>
@@ -106,7 +101,7 @@
             <param name="q_cover" value="86"/>
             <output name="output" file="rbh_none.tabular" ftype="tabular"/>
         </test>
-	<!-- push the coverage over the 86% level -->
+        <!-- push the coverage over the 86% level -->
         <test>
             <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
             <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
@@ -134,7 +129,7 @@
             <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 -->	
+        <!-- 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"/>
@@ -220,7 +215,7 @@
 Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
 or How To Use Sequence and Structure Information To Predict Protein
 Function. PLoS Comput Biol 4(10): e1000160.
-http://dx.doi.org/10.1371/journal.pcbi.1000160
+https://doi.org/10.1371/journal.pcbi.1000160
 
 The defaults are to require 70% sequence identity over the aligned region
 (using ``pident`` in the BLAST+ tabular output), and that the HSP alignment
@@ -235,12 +230,12 @@
 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015).
 NCBI BLAST+ integrated into Galaxy.
 *GigaScience* 4:39
-http://dx.doi.org/10.1186/s13742-015-0080-7
+https://doi.org/10.1186/s13742-015-0080-7
 
 Christiam Camacho et al. (2009).
 BLAST+: architecture and applications.
 *BMC Bioinformatics* 15;10:421.
-http://dx.doi.org/10.1186/1471-2105-10-421
+https://doi.org/10.1186/1471-2105-10-421
 
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
diff -r d8d9a9069586 -r 8f4500f6f2aa tools/blast_rbh/tool_dependencies.xml
--- a/tools/blast_rbh/tool_dependencies.xml	Wed Apr 19 07:44:47 2017 -0400
+++ b/tools/blast_rbh/tool_dependencies.xml	Tue Dec 06 15:53:36 2022 +0000
@@ -1,9 +1,9 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="biopython" version="1.67">
-        <repository changeset_revision="a42f244cce44" name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository name="package_biopython_1_67" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="a12f73c3b116"/>
     </package>
     <package name="blast" version="2.5.0">
-        <repository changeset_revision="5dd2b68c7d04" name="package_blast_plus_2_5_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository name="package_blast_plus_2_5_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" changeset_revision="5dd2b68c7d04"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file