# HG changeset patch
# User peterjc
# Date 1559582940 14400
# Node ID bbf14bb9607b4e0dba770e49fed659c8ce9b9045
# Parent  cee8f9005e43a156e4c587a9431e77755fbdb98c
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 89578746a1c5b29c84a173d8b2709f086f69a7b6

diff -r cee8f9005e43 -r bbf14bb9607b tools/mira4_0/mira4.py
--- a/tools/mira4_0/mira4.py	Wed Jul 11 12:35:35 2018 -0400
+++ b/tools/mira4_0/mira4.py	Mon Jun 03 13:29:00 2019 -0400
@@ -24,9 +24,12 @@
     # however there is some pipe error when doing that here.
     cmd = [mira_binary, "-v"]
     try:
-        child = subprocess.Popen(cmd, universal_newlines=True,
-                                 stdout=subprocess.PIPE,
-                                 stderr=subprocess.STDOUT)
+        child = subprocess.Popen(
+            cmd,
+            universal_newlines=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+        )
     except Exception as err:
         sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
         sys.exit(1)
@@ -36,31 +39,56 @@
 
 
 # Parse Command Line
-usage = """Galaxy MIRA4 wrapper script v%s - use as follows:
+usage = (
+    """Galaxy MIRA4 wrapper script v%s - use as follows:
 
 $ python mira4.py ...
 
 This will run the MIRA binary and collect its output files as directed.
-""" % WRAPPER_VER
+"""
+    % WRAPPER_VER
+)
 parser = OptionParser(usage=usage)
-parser.add_option("-m", "--manifest", dest="manifest",
-                  default=None, metavar="FILE",
-                  help="MIRA manifest filename")
-parser.add_option("--maf", dest="maf",
-                  default="-", metavar="FILE",
-                  help="MIRA MAF output filename")
-parser.add_option("--bam", dest="bam",
-                  default="-", metavar="FILE",
-                  help="Unpadded BAM output filename")
-parser.add_option("--fasta", dest="fasta",
-                  default="-", metavar="FILE",
-                  help="Unpadded FASTA output filename")
-parser.add_option("--log", dest="log",
-                  default="-", metavar="FILE",
-                  help="MIRA logging output filename")
-parser.add_option("-v", "--version", dest="version",
-                  default=False, action="store_true",
-                  help="Show version and quit")
+parser.add_option(
+    "-m",
+    "--manifest",
+    dest="manifest",
+    default=None,
+    metavar="FILE",
+    help="MIRA manifest filename",
+)
+parser.add_option(
+    "--maf", dest="maf", default="-", metavar="FILE", help="MIRA MAF output filename"
+)
+parser.add_option(
+    "--bam",
+    dest="bam",
+    default="-",
+    metavar="FILE",
+    help="Unpadded BAM output filename",
+)
+parser.add_option(
+    "--fasta",
+    dest="fasta",
+    default="-",
+    metavar="FILE",
+    help="Unpadded FASTA output filename",
+)
+parser.add_option(
+    "--log",
+    dest="log",
+    default="-",
+    metavar="FILE",
+    help="MIRA logging output filename",
+)
+parser.add_option(
+    "-v",
+    "--version",
+    dest="version",
+    default=False,
+    action="store_true",
+    help="Show version and quit",
+)
 options, args = parser.parse_args()
 manifest = options.manifest
 out_maf = options.maf
@@ -72,14 +100,20 @@
     mira_path = os.environ["MIRA4"]
     mira_binary = os.path.join(mira_path, "mira")
     if not os.path.isfile(mira_binary):
-        sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s"
-                 % (mira_binary, ", ".join(os.listdir(mira_path))))
+        sys.exit(
+            "Missing mira under $MIRA4, %r\nFolder contained: %s"
+            % (mira_binary, ", ".join(os.listdir(mira_path)))
+        )
     mira_convert = os.path.join(mira_path, "miraconvert")
     if not os.path.isfile(mira_convert):
-        sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
-                 % (mira_convert, ", ".join(os.listdir(mira_path))))
+        sys.exit(
+            "Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
+            % (mira_convert, ", ".join(os.listdir(mira_path)))
+        )
 else:
-    sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n")
+    sys.stderr.write(
+        "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
+    )
     mira_path = None
     mira_binary = "mira"
     mira_convert = "miraconvert"
@@ -178,8 +212,7 @@
         ref_fasta = "%s/%s_out_ReferenceStrain.padded.fasta" % (f, name)
 
     missing = False
-    for old, new in [(old_maf, out_maf),
-                     (old_fasta, out_fasta)]:
+    for old, new in [(old_maf, out_maf), (old_fasta, out_fasta)]:
         if not os.path.isfile(old):
             missing = True
         elif not new or new == "-":
@@ -245,20 +278,22 @@
     handle = open(out_log, "w")
 else:
     handle = open(os.devnull, "w")
-handle.write("======================== MIRA manifest (instructions) ========================\n")
+handle.write(
+    "======================== MIRA manifest (instructions) ========================\n"
+)
 m = open(manifest, "rU")
 for line in m:
     handle.write(line)
 m.close()
 del m
 handle.write("\n")
-handle.write("============================ Starting MIRA now ===============================\n")
+handle.write(
+    "============================ Starting MIRA now ===============================\n"
+)
 handle.flush()
 try:
     # Run MIRA
-    child = subprocess.Popen(cmd_list,
-                             stdout=handle,
-                             stderr=subprocess.STDOUT)
+    child = subprocess.Popen(cmd_list, stdout=handle, stderr=subprocess.STDOUT)
 except Exception as err:
     log_manifest(manifest)
     sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
@@ -272,7 +307,9 @@
 run_time = time.time() - start_time
 return_code = child.returncode
 handle.write("\n")
-handle.write("============================ MIRA has finished ===============================\n")
+handle.write(
+    "============================ MIRA has finished ===============================\n"
+)
 handle.write("MIRA took %0.2f hours\n" % (run_time / 3600.0))
 if return_code:
     print("MIRA took %0.2f hours" % (run_time / 3600.0))
@@ -288,22 +325,30 @@
 
 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
     handle.write("\n")
-    handle.write("====================== Extract Large Contigs failed ==========================\n")
+    handle.write(
+        "====================== Extract Large Contigs failed ==========================\n"  # noqa: E501
+    )
     e = open("MIRA_assembly/MIRA_d_results/ec.log", "rU")
     for line in e:
         handle.write(line)
     e.close()
-    handle.write("============================ (end of ec.log) =================================\n")
+    handle.write(
+        "============================ (end of ec.log) =================================\n"  # noqa: E501
+    )
     handle.flush()
 
 # print("Collecting output...")
 start_time = time.time()
 collect_output(temp, name, handle)
 collect_time = time.time() - start_time
-handle.write("MIRA took %0.2f hours; collecting output %0.2f minutes\n"
-             % (run_time / 3600.0, collect_time / 60.0))
-print("MIRA took %0.2f hours; collecting output %0.2f minutes\n"
-      % (run_time / 3600.0, collect_time / 60.0))
+handle.write(
+    "MIRA took %0.2f hours; collecting output %0.2f minutes\n"
+    % (run_time / 3600.0, collect_time / 60.0)
+)
+print(
+    "MIRA took %0.2f hours; collecting output %0.2f minutes\n"
+    % (run_time / 3600.0, collect_time / 60.0)
+)
 
 if os.path.isfile("MIRA_assembly/MIRA_d_results/ec.log"):
     # Treat as an error, but doing this AFTER collect_output
diff -r cee8f9005e43 -r bbf14bb9607b tools/mira4_0/mira4_bait.py
--- a/tools/mira4_0/mira4_bait.py	Wed Jul 11 12:35:35 2018 -0400
+++ b/tools/mira4_0/mira4_bait.py	Mon Jun 03 13:29:00 2019 -0400
@@ -18,9 +18,12 @@
     # however there is some pipe error when doing that here.
     cmd = [mira_binary, "-v"]
     try:
-        child = subprocess.Popen(cmd, universal_newlines=True,
-                                 stdout=subprocess.PIPE,
-                                 stderr=subprocess.STDOUT)
+        child = subprocess.Popen(
+            cmd,
+            universal_newlines=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+        )
     except Exception as err:
         sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
         sys.exit(1)
@@ -40,10 +43,14 @@
     mira_path = os.environ["MIRA4"]
     mira_binary = os.path.join(mira_path, "mirabait")
     if not os.path.isfile(mira_binary):
-        sys.exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s"
-                 % (mira_binary, ", ".join(os.listdir(mira_path))))
+        sys.exit(
+            "Missing mirabait under $MIRA4, %r\nFolder contained: %s"
+            % (mira_binary, ", ".join(os.listdir(mira_path)))
+        )
 else:
-    sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n")
+    sys.stderr.write(
+        "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
+    )
     mira_path = None
     mira_binary = "mirabait"
 
@@ -55,7 +62,16 @@
     sys.exit(0)
 
 
-format, output_choice, strand_choice, kmer_length, min_occurance, bait_file, in_file, out_file = sys.argv[1:]
+(
+    format,
+    output_choice,
+    strand_choice,
+    kmer_length,
+    min_occurance,
+    bait_file,
+    in_file,
+    out_file,
+) = sys.argv[1:]
 
 if format.startswith("fastq"):
     format = "fastq"
@@ -67,9 +83,20 @@
 assert out_file.endswith(".dat")
 out_file_stem = out_file[:-4]
 
-cmd_list = [mira_binary, "-f", format, "-t", format,
-            "-k", kmer_length, "-n", min_occurance,
-            bait_file, in_file, out_file_stem]
+cmd_list = [
+    mira_binary,
+    "-f",
+    format,
+    "-t",
+    format,
+    "-k",
+    kmer_length,
+    "-n",
+    min_occurance,
+    bait_file,
+    in_file,
+    out_file_stem,
+]
 if output_choice == "pos":
     pass
 elif output_choice == "neg":
@@ -90,9 +117,12 @@
 start_time = time.time()
 try:
     # Run MIRA
-    child = subprocess.Popen(cmd_list, universal_newlines=True,
-                             stdout=subprocess.PIPE,
-                             stderr=subprocess.STDOUT)
+    child = subprocess.Popen(
+        cmd_list,
+        universal_newlines=True,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.STDOUT,
+    )
 except Exception as err:
     sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
     sys.exit(1)
@@ -105,8 +135,7 @@
 
 if return_code:
     sys.stderr.write(stdout)
-    sys.exit("Return error code %i from command:\n%s" % (return_code, cmd),
-             return_code)
+    sys.exit("Return error code %i from command:\n%s" % (return_code, cmd), return_code)
 
 # Capture output
 out_tmp = out_file_stem + "." + format
diff -r cee8f9005e43 -r bbf14bb9607b tools/mira4_0/mira4_convert.py
--- a/tools/mira4_0/mira4_convert.py	Wed Jul 11 12:35:35 2018 -0400
+++ b/tools/mira4_0/mira4_convert.py	Mon Jun 03 13:29:00 2019 -0400
@@ -29,8 +29,9 @@
     # Avoid using shell=True when we call subprocess to ensure if the Python
     # script is killed, so too is the child process.
     try:
-        child = subprocess.Popen(cmd, universal_newlines=True,
-                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+        child = subprocess.Popen(
+            cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
+        )
     except Exception as err:
         sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
     # Use .communicate as can get deadlocks with .wait(),
@@ -39,9 +40,14 @@
     if return_code:
         cmd_str = " ".join(cmd)  # doesn't quote spaces etc
         if stderr and stdout:
-            sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
+            sys.exit(
+                "Return code %i from command:\n%s\n\n%s\n\n%s"
+                % (return_code, cmd_str, stdout, stderr)
+            )
         else:
-            sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
+            sys.exit(
+                "Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)
+            )
 
 
 def get_version(mira_binary):
@@ -50,9 +56,7 @@
     # however there is some pipe error when doing that here.
     cmd = [mira_binary, "-v"]
     try:
-        child = subprocess.Popen(cmd,
-                                 stdout=subprocess.PIPE,
-                                 stderr=subprocess.STDOUT)
+        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
     except Exception as err:
         sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
         sys.exit(1)
@@ -62,43 +66,63 @@
 
 
 # Parse Command Line
-usage = """Galaxy MIRA4 wrapper script v%s - use as follows:
+usage = (
+    """Galaxy MIRA4 wrapper script v%s - use as follows:
 
 $ python mira4_convert.py ...
 
 This will run the MIRA miraconvert binary and collect its output files as directed.
-""" % WRAPPER_VER
+"""
+    % WRAPPER_VER
+)
 parser = OptionParser(usage=usage)
-parser.add_option("--input", dest="input",
-                  default=None, metavar="FILE",
-                  help="MIRA input filename")
-parser.add_option("-x", "--min_length", dest="min_length",
-                  default="0",
-                  help="Minimum contig length")
-parser.add_option("-y", "--min_cover", dest="min_cover",
-                  default="0",
-                  help="Minimum average contig coverage")
-parser.add_option("-z", "--min_reads", dest="min_reads",
-                  default="0",
-                  help="Minimum reads per contig")
-parser.add_option("--maf", dest="maf",
-                  default="", metavar="FILE",
-                  help="MIRA MAF output filename")
-parser.add_option("--ace", dest="ace",
-                  default="", metavar="FILE",
-                  help="ACE output filename")
-parser.add_option("--bam", dest="bam",
-                  default="", metavar="FILE",
-                  help="Unpadded BAM output filename")
-parser.add_option("--fasta", dest="fasta",
-                  default="", metavar="FILE",
-                  help="Unpadded FASTA output filename")
-parser.add_option("--cstats", dest="cstats",
-                  default="", metavar="FILE",
-                  help="Contig statistics filename")
-parser.add_option("-v", "--version", dest="version",
-                  default=False, action="store_true",
-                  help="Show version and quit")
+parser.add_option(
+    "--input", dest="input", default=None, metavar="FILE", help="MIRA input filename"
+)
+parser.add_option(
+    "-x", "--min_length", dest="min_length", default="0", help="Minimum contig length"
+)
+parser.add_option(
+    "-y",
+    "--min_cover",
+    dest="min_cover",
+    default="0",
+    help="Minimum average contig coverage",
+)
+parser.add_option(
+    "-z", "--min_reads", dest="min_reads", default="0", help="Minimum reads per contig"
+)
+parser.add_option(
+    "--maf", dest="maf", default="", metavar="FILE", help="MIRA MAF output filename"
+)
+parser.add_option(
+    "--ace", dest="ace", default="", metavar="FILE", help="ACE output filename"
+)
+parser.add_option(
+    "--bam", dest="bam", default="", metavar="FILE", help="Unpadded BAM output filename"
+)
+parser.add_option(
+    "--fasta",
+    dest="fasta",
+    default="",
+    metavar="FILE",
+    help="Unpadded FASTA output filename",
+)
+parser.add_option(
+    "--cstats",
+    dest="cstats",
+    default="",
+    metavar="FILE",
+    help="Contig statistics filename",
+)
+parser.add_option(
+    "-v",
+    "--version",
+    dest="version",
+    default=False,
+    action="store_true",
+    help="Show version and quit",
+)
 options, args = parser.parse_args()
 if args:
     sys.exit("Expected options (e.g. --input example.maf), not arguments")
@@ -114,16 +138,22 @@
     mira_path = os.environ["MIRA4"]
     mira_convert = os.path.join(mira_path, "miraconvert")
     if not os.path.isfile(mira_convert):
-        sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
-                 % (mira_convert, ", ".join(os.listdir(mira_path))))
+        sys.exit(
+            "Missing miraconvert under $MIRA4, %r\nFolder contained: %s"
+            % (mira_convert, ", ".join(os.listdir(mira_path)))
+        )
 else:
-    sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n")
+    sys.stderr.write(
+        "DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n"
+    )
     mira_path = None
     mira_convert = "miraconvert"
 
 mira_convert_ver = get_version(mira_convert)
 if not mira_convert_ver.strip().startswith("4.0"):
-    sys.exit("This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert))
+    sys.exit(
+        "This wrapper is for MIRA V4.0, not:\n%s\n%s" % (mira_convert_ver, mira_convert)
+    )
 if options.version:
     print("%s, MIRA wrapper version %s" % (mira_convert_ver, WRAPPER_VER))
     sys.exit(0)
diff -r cee8f9005e43 -r bbf14bb9607b tools/mira4_0/mira4_make_bam.py
--- a/tools/mira4_0/mira4_make_bam.py	Wed Jul 11 12:35:35 2018 -0400
+++ b/tools/mira4_0/mira4_make_bam.py	Mon Jun 03 13:29:00 2019 -0400
@@ -10,10 +10,13 @@
 
 def run(cmd, log_handle):
     try:
-        child = subprocess.Popen(cmd, shell=True,
-                                 universal_newlines=True,
-                                 stdout=subprocess.PIPE,
-                                 stderr=subprocess.STDOUT)
+        child = subprocess.Popen(
+            cmd,
+            shell=True,
+            universal_newlines=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.STDOUT,
+        )
     except Exception as err:
         sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
         # TODO - call clean up?
@@ -32,17 +35,27 @@
 
 
 def depad(fasta_file, sam_file, bam_file, log_handle):
-    log_handle.write("\n================= Converting MIRA assembly from SAM to BAM ===================\n")
+    log_handle.write(
+        "\n================= Converting MIRA assembly from SAM to BAM ===================\n"  # noqa: E501
+    )
     # Also doing SAM to (uncompressed) BAM during depad
-    bam_stem = bam_file + ".tmp"  # Have write permissions and want final file in this folder
-    cmd = 'samtools depad -S -u -T "%s" "%s" | samtools sort - "%s"' % (fasta_file, sam_file, bam_stem)
+    bam_stem = (
+        bam_file + ".tmp"
+    )  # Have write permissions and want final file in this folder
+    cmd = 'samtools depad -S -u -T "%s" "%s" | samtools sort - "%s"' % (
+        fasta_file,
+        sam_file,
+        bam_stem,
+    )
     return_code = run(cmd, log_handle)
     if return_code:
         return "Error %i from command:\n%s" % (return_code, cmd)
     if not os.path.isfile(bam_stem + ".bam"):
         return "samtools depad or sort failed to produce BAM file"
 
-    log_handle.write("\n====================== Indexing MIRA assembly BAM file =======================\n")
+    log_handle.write(
+        "\n====================== Indexing MIRA assembly BAM file =======================\n"  # noqa: E501
+    )
     cmd = 'samtools index "%s.bam"' % bam_stem
     return_code = run(cmd, log_handle)
     if return_code:
@@ -60,7 +73,9 @@
     if not os.path.isfile(fasta_file):
         return "Missing padded FASTA file: %r" % fasta_file
 
-    log_handle.write("\n====================== Converting MIRA assembly to SAM =======================\n")
+    log_handle.write(
+        "\n====================== Converting MIRA assembly to SAM =======================\n"  # noqa: E501
+    )
     tmp_dir = tempfile.mkdtemp()
     sam_file = os.path.join(tmp_dir, "x.sam")
 
diff -r cee8f9005e43 -r bbf14bb9607b tools/mira4_0/mira4_validator.py
--- a/tools/mira4_0/mira4_validator.py	Wed Jul 11 12:35:35 2018 -0400
+++ b/tools/mira4_0/mira4_validator.py	Mon Jun 03 13:29:00 2019 -0400
@@ -36,7 +36,9 @@
             try:
                 min_size_int = int(min_size)
                 if min_size_int < 0:
-                    err["min_size"] = "Minumum size must not be negative (%i)" % min_size_int
+                    err["min_size"] = (
+                        "Minumum size must not be negative (%i)" % min_size_int
+                    )
                     min_size = None  # Avoid doing comparison below
             except ValueError:
                 err["min_size"] = "Minimum size is not an integer (%s)" % min_size
@@ -46,14 +48,19 @@
             try:
                 max_size_int = int(max_size)
                 if max_size_int < 0:
-                    err["max_size"] = "Maximum size must not be negative (%i)" % max_size_int
+                    err["max_size"] = (
+                        "Maximum size must not be negative (%i)" % max_size_int
+                    )
                     max_size = None  # Avoid doing comparison below
             except ValueError:
                 err["max_size"] = "Maximum size is not an integer (%s)" % max_size
                 max_size = None  # Avoid doing comparison below
 
         if min_size and max_size and min_size_int > max_size_int:
-            msg = "Minimum size must be less than maximum size (%i vs %i)" % (min_size_int, max_size_int)
+            msg = "Minimum size must be less than maximum size (%i vs %i)" % (
+                min_size_int,
+                max_size_int,
+            )
             err["min_size"] = msg
             err["max_size"] = msg
 
diff -r cee8f9005e43 -r bbf14bb9607b tools/mira4_0/repository_dependencies.xml
--- a/tools/mira4_0/repository_dependencies.xml	Wed Jul 11 12:35:35 2018 -0400
+++ b/tools/mira4_0/repository_dependencies.xml	Mon Jun 03 13:29:00 2019 -0400
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format).">
-    <repository changeset_revision="2bd1f1175fb2" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-</repositories>
+    <repository changeset_revision="65ea1ef0181d" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
+</repositories>
\ No newline at end of file
diff -r cee8f9005e43 -r bbf14bb9607b tools/mira4_0/tool_dependencies.xml
--- a/tools/mira4_0/tool_dependencies.xml	Wed Jul 11 12:35:35 2018 -0400
+++ b/tools/mira4_0/tool_dependencies.xml	Mon Jun 03 13:29:00 2019 -0400
@@ -1,9 +1,9 @@
-<?xml version="1.0"?>
+<?xml version="1.0" ?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
     <package name="MIRA" version="4.0.2">
-        <repository changeset_revision="b4efe6c4acf7" name="package_mira_4_0_2" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b4efe6c4acf7" name="package_mira_4_0_2" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu"/>
     </package>
-</tool_dependency>
+</tool_dependency>
\ No newline at end of file