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author xzk-
date Fri, 15 Jun 2012 14:18:08 -0400
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files GU_files/._gu.py GU_files/._gu.xml GU_files/gu.py GU_files/gu.xml
diffstat 4 files changed, 661 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GU_files/gu.py	Fri Jun 15 14:18:08 2012 -0400
@@ -0,0 +1,562 @@
+#!/usr/local/bin/python 
+#
+# gu - Gene Unification Pipeline
+#
+# This pipeline compares two GFF input files for coordinate overlaps, and
+# bucketizes the overlapping feature pairs. The comparison step takes two lists 
+# of features [a1, a2, ...], [b1, b2, ...], outputs all feature pairs [ai, bj] such
+# that ai overlaps bj.
+#
+# These feature pairs form the edges in a bipartite graph of overlapping
+# a's and b's. Bucketization finds the connected components of the graph
+# and segregates those components (or clusters) into buckets, according to 
+# how many a's and b's there are in the cluster (one-to-one, one-to-many, etc).
+# The buckets are output to separate files (bucket_1-1.txt, bucket_1-n.txt, ...)
+#
+# There is one line output per overlapping pair [ai,bj]. This line contains
+# all the columns of ai and bj plus three additional columns about the cluster
+# to which this pair belongs. In detail:
+#	1. The id of the cluster (connected component) to which this pair belongs.
+#	2. The bucket label (e.g. "n-1").
+#	3. The actual counts of a's and b's in the cluster, e.g. "3-1" for 3 a's and 1 b.
+#	4- All of the columns of ai followed by all of the columns of bj.
+#
+# GU operates in one of two modes. The above description corresponds to 'no-aggregate'
+# mode: the overlapping features are bucketized directly. Sometimes, however, you want
+# the results aggregated to a higher level. For example, you may have files of exons,
+# but what you want is buckets of overlapping genes. For this, there is 'aggregate' mode,
+# in which lists of overlapping exons (for example) are turned into lists of overlapping genes
+# before being bucketized. Because aggregation loses the details of the underlying features,
+# the output format is somewhat different from no-aggregate mode. 
+# 
+#--------------------------------------------
+
+import sys
+import time
+import string
+from tempfile import mkstemp
+import os
+import os.path
+from TableTools import TA,TB,TD,TF,TI,TJ,TP,TS,TU,TX,FJ
+from optparse import OptionParser
+import re
+
+USAGE="%prog [options] --f1 file1.gff --f2 file2.gff\n(For help, use -h option.)"
+
+def now():
+	return time.asctime(time.localtime(time.time()))
+
+class GUPipeline :
+    #----------------------------------------------------
+    def __init__(self, argv):
+	# 1. initialize the option parser
+	#
+	self.argv = argv
+	self.parser = OptionParser(USAGE)
+	self.tempfiles = []
+	self.types1 = []
+	self.types2 = []
+
+	self.parser.add_option("-1", "--f1", "--file1",
+		dest="file1",
+		metavar="FILE1",
+		default=None,
+		help="The first GFF file.")
+
+	self.parser.add_option("-2", "--f2", "--file2",
+		dest="file2",
+		metavar="FILE2",
+		default=None,
+		help="The second GFF file.")
+
+	self.parser.add_option("-k", "--minOverlap", 
+		dest="k",
+		metavar=" AMT",
+		default="1",
+		help="The minimum required overlap. (Default: 1)")
+
+	#self.parser.set_defaults(mode="advanced")
+	self.parser.add_option("--t1", 
+	    dest="types1",
+	    action="append",
+	    metavar="GFFTYPE",
+	    default=[],
+	    help="A GFF type to select from file 1. Repeatable. (Default = all types)" )
+
+	self.parser.add_option("--t2", 
+	    dest="types2",
+	    action="append",
+	    metavar="GFFTYPE",
+	    default=[],
+	    help="A GFF type to select from file 2. Repeatable.(Default = all types)" )
+
+	self.parser.add_option("--nt1", 
+	    dest="notTypes1",
+	    action="append",
+	    metavar="GFFTYPE",
+	    default=[],
+	    help="A GFF type to FILTER OUT of file 1. Repeatable. (Default = filters no types)" )
+
+	self.parser.add_option("--nt2", 
+	    dest="notTypes2",
+	    action="append",
+	    metavar="GFFTYPE",
+	    default=[],
+	    help="A GFF type to filter out of file 2. Repeatable.(Default = filters no types)" )
+
+	self.parser.add_option("--ire", 
+	    dest="ire",
+	    metavar="REGEX",
+	    default=None,
+	    help="A regular expression that will be used to extract ids from column 9. " +
+	      "(Also: what you'll feel as you try to get this parameter right...) " +
+	      "Only applicable in aggregate mode. You can specify different patterns for " +
+	      "inputs 1 and 2 by specifying --ire1 and --ire2 instead. " +
+	      "Example: to aggregate both inputs by MGI id: --ire 'MGI:[0-9]+'. " +
+	      "Example: to aggregate input1 by MGI id and input 2 by VEGA id: " +
+	      "--ire1 'MGI:[0-9]+'  --ire2 'OTTMUSG[0-9]+'. " +
+	      "Advanced usage: Sometimes you need to define a regular expression where the actual " +
+	      "id you wish to extract is a sub-part of the whole pattern. This is called a 'capture'. " +
+	      "To capture the id, surround that part of the pattern with the magic symbols " +
+	      "'(?P<id>' and ')'. For example, suppose you want to capture the MGI id only when it's " +
+	      "part of a dbref attribute like this: 'Dbxref=MGI:MGI:012345;'. You could use the following " +
+	      "regular expression: 'Dbxref=MGI:(?P<id>MGI:[0-9]+);'."
+	    )
+
+	self.parser.add_option("--ire1", 
+	    dest="ire1",
+	    metavar="REGEX",
+	    default=None,
+	    help="Specify regex for input 1 only. See --ire."
+	    )
+
+	self.parser.add_option("--ire2", 
+	    dest="ire2",
+	    metavar="REGEX",
+	    default=None,
+	    help="Specify regex for input 2 only. See --ire."
+	    )
+
+	self.parser.add_option("-i", "--ignoreStrand", 
+	    dest="ignoreStrand",
+	    action="store_true",
+	    default = False,
+	    help="Ignore strand when determining overlaps (Default = strands must match)")
+
+	self.parser.add_option("-n", "--noAggregate", 
+	    dest="noAggregate",
+	    action="store_true",
+	    default = False,
+	    help="Do not aggregate features. Opposite of -a.")
+
+	self.parser.add_option("-C", "--chrMatchLoose", 
+	    dest="chrMatchLoose",
+	    action="store_true",
+	    default = False,
+	    help="If specified, chromosome matching is 'loose'. Otherwise it is exact. " + \
+		"In loose matching, leading 'chr' is removed from chromosome field, " + \
+		"so that '19' matches 'Chr19'. ")
+
+	self.parser.add_option("-s", "--noSelfHits", 
+	    dest="noSelfHits",
+	    action="store_true",
+	    default = False,
+	    help="Ignore self-hit in overlap detection. (default: reports self-hits)")
+
+	self.parser.add_option("-d", "--od", 
+	    dest="outDir",
+	    metavar="DIRECTORY",
+	    default=".",
+	    help="Path of output directory. (Default = current directory)")
+
+	self.parser.add_option("-t", 
+	    dest="template",
+	    metavar="TEMPLATE",
+	    default="bucket_%s.txt",
+	    help="Template string for naming output bucket files. " + \
+	    "Must contain the substring '%s', which is replaced by the bucket class. " + \
+	    "The classes are: '1-0', '0-1', '1-1', '1-n', 'n-1', 'n-m'. " + \
+	    "(Default: bucket_%s.txt)")
+
+	self.parser.add_option("-l", "--lf", "--logFile",
+	    dest="logFile",
+	    metavar="FILE",
+	    default=None,
+	    help="Log file. (Default = writes to stderr)")
+
+	# 2. Parse the command line
+	#
+	(self.options,xxx) = self.parser.parse_args(argv)
+
+	# 3. Validate the args
+	#
+	if self.options.logFile is not None:
+	    sys.stderr = open(self.options.logFile, 'a')
+
+	if self.options.file1 is None \
+	or self.options.file2 is None:
+	    self.parser.error("Must specify both --f1 and --f2.")
+
+	if not os.path.isdir(self.options.outDir):
+	    self.parser.error("Output directory " + self.options.outDir + \
+	    	" does not exist or is not a directory.")
+
+	self.types1 = str( self.options.types1 ).lower()
+	self.types2 = str( self.options.types2 ).lower()
+	self.notTypes1 = str( self.options.notTypes1 ).lower()
+	self.notTypes2 = str( self.options.notTypes2 ).lower()
+
+	self.minOverlap = self.options.k
+
+	if not '%s' in self.options.template:
+	    self.options.template += '%s'
+
+	self.options.template = \
+	        os.path.join( self.options.outDir, self.options.template)
+	
+	if self.options.chrMatchLoose:
+	    self.options.chrMatchExpr = "[re.sub('^(?i)chr(om(osome)?)?', '', IN[1])]+IN[2:]"
+	else:
+	    self.options.chrMatchExpr = "IN[1:]"
+	
+	self.options.guDir = os.path.split(__file__)[0]
+	self.options.guUtilFile = os.path.join(self.options.guDir,'guUtil.py')
+
+
+	# local function
+	def groomRe(name, default):
+	    r = getattr(self.options, name)
+	    if r is None:
+		r = default
+	    if "(?P<id>" not in r:
+		r = "(?P<id>%s)" % r
+	    r = "r'%s'" % r
+	    setattr(self.options, name, r )
+	    self.debug('%s=%s\n'%(name,r))
+
+	if self.options.ire is None:
+	    self.options.ire = r' *(gene_?(id)?|id)? *[=:]? *"?(?P<id>[^"; ]+)"?'
+	dflt = self.options.ire
+	groomRe('ire1',dflt)
+	groomRe('ire2',dflt)
+
+	
+    #----------------------------------------------------
+    def mkTmp(self,preserve=False):
+	tf = mkstemp()
+	os.close(tf[0])
+	if not preserve:
+	    self.tempfiles.append(tf[1])
+	return tf[1]
+
+    #----------------------------------------------------
+    def cleanupTempFiles(self):
+	for tf in self.tempfiles:
+	    os.remove(tf)
+
+    #----------------------------------------------------
+    def debug(self,s,ts=False):
+	if ts:
+	    sys.stderr.write(now()+': ')
+	sys.stderr.write(s)
+
+    #----------------------------------------------------
+    def execStep(self, tool, args):
+	self.debug( tool.__name__ + " " + string.join(args, " ") + "\n", True)
+    	t = tool(args)
+	t.go()
+	t.closeFiles()
+	return t.nOutputRows
+
+    #----------------------------------------------------
+    def go_noAggregate(self):
+
+	### Select rows from first file.
+
+	args = [
+	    "--file1="+self.options.file1,
+	    self.options.chrMatchExpr,
+	    ]
+
+	if len(self.options.types1) > 0:
+	    args.append( "?string.lower(IN[3]) in %s" % self.types1 )
+
+	if len(self.options.notTypes1) > 0:
+	    args.append( "?string.lower(IN[3]) not in %s" % self.notTypes1 )
+
+	if len(args) > 2:
+	    f1 = self.mkTmp()
+	    args.append( "--out-file=" + f1 )
+	    self.execStep(TF, args)
+	else:
+	    f1 = self.options.file1
+
+	### Select rows from second file.
+
+	args = [
+	    "--file1="+self.options.file2,
+	    self.options.chrMatchExpr,
+	    ]
+
+	if len(self.options.types2) > 0:
+	    args.append( "?string.lower(IN[3]) in %s" % self.types2 )
+
+	if len(self.options.notTypes2) > 0:
+	    args.append( "?string.lower(IN[3]) not in %s" % self.notTypes2 )
+
+	if len(args) > 2:
+	    f2 = self.mkTmp()
+	    args.append( "--out-file=" + f2 )
+	    self.execStep(TF, args)
+	else:
+	    f2 = self.options.file2
+
+	### find overlapping features. 
+
+	overlaps=self.mkTmp()
+	args = [
+	    "-1", f1,
+	    "-2", f2,
+	    "-s", "both",
+	    "-k", self.minOverlap,
+	    "-o", overlaps,
+	    ]
+	if self.options.ignoreStrand:
+	    args = args + ["--columns1", "1,4,5"]
+	novl = self.execStep(FJ, args)
+
+	if self.options.noSelfHits:
+	    xxx = overlaps
+	    overlaps = self.mkTmp()
+	    args = [ 
+	    	"?IN[10]!=IN[19]",
+		"-1", xxx,
+		"-o", overlaps,
+		]
+	    novl = self.execStep(TF, args)
+	    #self.debug("FJ out: " + xxx)
+	    #self.debug("TF out: " + overlaps)
+	    #os.system("diff %s %s" %(xxx,overlaps))
+
+
+	if novl == 0:
+	    self.debug("No overlapping features detected.\n")
+
+	### bucketize the pairs.
+
+	bucketized=self.mkTmp()
+	self.execStep(TB, [
+	    "--file1=" + overlaps,
+	    "--k1=10",
+	    "--k2=19",
+	    "-t"+bucketized,
+	    "IN[1:]",
+	    "int(IN[11]!=IN[20])",	## compute column: 0==same strands 1==diff
+	    "int(string.lower(IN[7])!='gene')",	## compute column: 0==all genes 1==nongene
+	    ])
+
+	sorted = self.mkTmp()
+	self.execStep(TS, [
+	    "--file1=" + bucketized,
+	    "-k 3",
+	    "-k 1",
+	    "--out-file=" + sorted,
+	    ])
+
+	self.execStep(TP, [
+	    "--file1=" + sorted,
+	    "-o" + self.options.template,
+	    "-p 3",
+	    ])
+
+	### Bucketization did not generate 1-0 and 0-1 buckets
+	### (because we only fed it overlapping pairs).
+	### Generate these buckets by diff'ing the inputs
+	### against the fjoin output.
+
+	self.execStep(TD, [
+	    "--file1=" + f1,
+	    "--k1=9",
+	    "--file2=" + bucketized,
+	    "--k2=13",
+	    "--out-file=" + (self.options.template%"1-0") ])
+
+	self.execStep(TD, [
+	    "--file1=" + f2,
+	    "--k1=9",
+	    "--file2=" + bucketized,
+	    "--k2=22",
+	    "--out-file=" + (self.options.template%"0-1") ])
+
+    #----------------------------------------------------
+    def go_aggregate(self):
+	
+	# Select rows from first file, and extract feature ids.
+	f1 = self.mkTmp()
+	args = [
+	    "--file1="+self.options.file1,
+	    "--exec-file="+self.options.guUtilFile,
+	    ]
+	if len(self.options.types1) > 0:
+	    args.append( "?string.lower(IN[3]) in %s" % self.types1 )
+	if len(self.options.notTypes1) > 0:
+	    args.append( "?string.lower(IN[3]) not in %s" % self.notTypes1 )
+	args += [
+	    "IN[1:9]",
+	    'extractID(IN[9],%s)'%self.options.ire1,
+	    "--out-file=" + f1
+	    ]
+
+	self.execStep(TF, args)
+
+	# Select rows from second file, and extract feature ids.
+	f2 = self.mkTmp()
+	args = [
+	    "--file1="+self.options.file2,
+	    "--exec-file="+self.options.guUtilFile,
+	    ]
+	if len(self.options.types2) > 0:
+	    args.append( "?string.lower(IN[3]) in %s" % self.types2 )
+	if len(self.options.notTypes2) > 0:
+	    args.append( "?string.lower(IN[3]) not in %s" % self.notTypes2 )
+	args += [
+	    "IN[1:9]",
+	    'extractID(IN[9],%s)'%self.options.ire2,
+	    "--out-file=" + f2
+	    ]
+	self.execStep(TF, args)
+
+	# Find the distinct higher-level features in file1 and count the base features
+	genes1=os.path.join(self.options.outDir, "features1.txt")
+	self.execStep(TA, [
+	    "--file1="+f1,
+	    "-g9",		# id
+	    "-acount",		# num. lines w/ this id
+	    "-afirst:1",	# first chr
+	    "-amin:4",		# min start val
+	    "-amax:5",		# max end val
+	    "-afirst:7",	# first strand
+	    "--out-file=" + genes1
+	    ])
+
+	# Find the unique genes in file2 and count the exons
+	genes2=os.path.join(self.options.outDir, "features2.txt")
+	self.execStep(TA, [
+	    "--file1="+f2,
+	    "-g9",
+	    "-acount",
+	    "-afirst:1",
+	    "-amin:4",
+	    "-amax:5",
+	    "-afirst:7",
+	    "--out-file=" + genes2
+	    ])
+
+	# Find all overlapping feature pairs.
+	ovlExons=self.mkTmp()
+	args = [
+	    "-1", f1,
+	    "-2", f2,
+	    "-o", ovlExons,
+	    "-s", "both",
+	    "-k", self.minOverlap,
+	    ]
+	if self.options.ignoreStrand:
+	    args = args + ["--columns1", "1,4,5"]
+	novl = self.execStep(FJ, args)
+
+	if self.options.noSelfHits:
+	    xxx = ovlExons
+	    ovlExons = self.mkTmp()
+	    args = [ 
+	    	"?IN[10] != IN[19]",
+		"-1", xxx,
+		"-o", ovlExons,
+		]
+	    novl = self.execStep(TF, args)
+
+	if novl == 0:
+	    self.debug("No overlapping features detected.\n")
+
+	#  Aggregate overlapping feature pairs into higher-level overlaps.
+	#  Count the base features involved.
+	ovlGenes = self.mkTmp()
+	self.execStep(TA, [
+	    "-g10,19",
+	    "-acount:5",
+	    "-acount:14",
+	    "--file1="+ovlExons,
+	    "--out-file=" + ovlGenes
+	    ])
+
+	#  Join with genes1 to pull in total exon counts.
+	#    Do an outer join so that every gene in genes1 is
+	#    represented.
+	tmp1 = self.mkTmp()
+	self.execStep(TJ, [
+	    "--file1=" + ovlGenes,
+	    "--file2=" + genes1,
+	    "--k1=1",
+	    "--k2=1",
+	    "--right",
+	    "-n.",
+	    "--out-file=" + tmp1
+	    ])
+
+	#  Join with genes2 to pull in total exon counts.
+	#    Do a bidi-outer join so that every gene in genes2 is
+	#    represented, as is every gene in genes1..
+	tmp2 = self.mkTmp()
+	self.execStep(TJ, [
+	    "--file1=" + tmp1,
+	    "--file2=" + genes2,
+	    "--k1=2",
+	    "--k2=1",
+	    "--left",
+	    "--right",
+	    "-n.",
+	    "--out-file=" + tmp2
+	    ])
+
+	#  Filter for final output formatting.
+	tmp3 = self.mkTmp()
+	self.execStep(TF, [
+	    "--file1=" + tmp2,
+	    "--out-file=" + tmp3,
+	    "IN[7]=='.' and IN[13] or IN[7]" ,
+	    "IN[10]=='.' and IN[16] or IN[16]=='.' and IN[10] or IN[16]==IN[10] and IN[16] or '???'",
+	    "IN[5]", "IN[3]", "IN[6]", "IN[8]", "IN[9]", "IN[10]",
+	    "IN[11]", "IN[4]", "IN[12]", "IN[14]", "IN[15]", "IN[16]",
+	    ])
+
+	#  Bucketize the overlapping genes. Output separate file for
+	# each bucket.
+	self.execStep(TB, [
+	    "--file1=" + tmp3,
+	    "--k1=3",
+	    "--k2=9",
+	    "-n.",
+	    "-t" + self.options.template,
+	    "IN[1:3]", "IN[4:]",   ## remove the bucket id column
+	    ])
+
+    def go(self):
+	self.debug("======================================\n")
+	self.debug("Starting GU pipeline\n", True)
+	self.debug("Command line:\n%s\n" % (" ".join(self.argv)))
+
+	if(self.options.noAggregate):
+	    self.go_noAggregate()
+	else:
+	    self.go_aggregate()
+
+	self.debug("Pipeline completed.\n", True)
+	self.debug("Cleaning up...\n")
+
+	#  Delete the temp files
+	#self.cleanupTempFiles()
+	self.debug("Goodbye.\n\n")
+
+#--------------------------------
+GUPipeline(sys.argv).go()
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GU_files/gu.xml	Fri Jun 15 14:18:08 2012 -0400
@@ -0,0 +1,99 @@
+<tool id="gu" name="GU" version="0.0.1">
+  <description>Comparing genomic information overlap between two files</description>
+  <command interpreter="python">
+    GU.py
+        --f1 $input1
+  		--f2 $input2
+  		--minOverlap $minOverlap
+  		--ignoreStrand $ignoreStrand
+  		--noSelfHits $noSelfHits
+  		--chrMatchLoose $chrMatching
+  		--noAggregate $noAggregate
+  		$selectType1
+  		$selectType2
+  		$NotSelectType1
+  		$NotSelectType2
+  		-l LOG
+  </command>
+  <inputs>
+    <param format="tabular" name="input1" type="data" label="First Data File"/>
+    <param format="tabular" name="input2" type="data" label="Second Data File"/>
+  	<param name="minOverlap" type="text" size="5" value="1" label="Minimum Overlap" help="The minimum coordinate required overlap."/>
+	<param name="noSelfHits" type="select" label="Ignore Self Hits in Overlap Detection" help="Ignore self-hit in overlap detection. (default: reports self-hits)">
+		<option value="False">False</option>
+		<option value="True">True</option>
+    </param>
+  	<param name="ignoreStrand" type="select" label="Ignore Strand" help="Ignore strand when determining overlaps (Default = strands must match).">
+  		<option value="False">No</option>
+		<option value="True">Yes</option>
+    </param>
+	<param name="noSelfHits" type="select" label="Ignore Self Hits in Overlap Detection" help="If specified, chromosome matching is 'loose'. Otherwise it is exact. In loose matching, leading 'chr' is removed from chromosome field, so that '19' matches 'Chr19'.">
+		<option value="False">Off</option>
+		<option value="True">On</option>
+    </param>
+	<param name="chrMatching" type="select" label="Loose Chromosome Matching">
+		<option value="False">Off</option>
+		<option value="True">On</option>
+    </param>
+    <param name="noAggregate" type="select" label="Aggregate Mode" help="Default is non-aggregate mode.">
+    	<option value="False">Off</option>
+    	<option value="True">On</option>
+    </param>
+    <param name="selectType1" type="select" label="Select First Feature to Include" multiple="True" help="A GFF type to select from file 1.">
+  		<option value="">All</option>
+  		<option value="--t1 Exon">Exon</option>
+  		<option value="--t1 Gene">Gene</option>
+  		<option value="--t1 Pseudogene">Pseudogene</option>
+  		<option value="--t1 QTL">QTL</option>
+    </param>
+    <param name="selectType2" type="select" label="Select Second Feature to Include" multiple="True" help="A GFF type to select from file 2.">
+  		<option value="">All</option>
+  		<option value="--t1 Exon">Exon</option>
+  		<option value="--t1 Gene">Gene</option>
+  		<option value="--t1 Pseudogene">Pseudogene</option>
+  		<option value="--t1 QTL">QTL</option>
+    </param>
+    <param name="NotSelectType1" type="select" label="Select First Feature to Exclude" multiple="True" help="A GFF type to select from file 1.">
+  		<option value="">All</option>
+  		<option value="--t1 Exon">Exon</option>
+  		<option value="--t1 Gene">Gene</option>
+  		<option value="--t1 Pseudogene">Pseudogene</option>
+  		<option value="--t1 QTL">QTL</option>
+    </param>
+    <param name="NotSelectType2" type="select" label="Select Second Feature to Exclude" multiple="True" help="A GFF type to select from file 2.">
+  		<option value="">All</option>
+  		<option value="--t1 Exon">Exon</option>
+  		<option value="--t1 Gene">Gene</option>
+  		<option value="--t1 Pseudogene">Pseudogene</option>
+  		<option value="--t1 QTL">QTL</option>
+    </param>        
+  </inputs>
+  <help>
+.. class:: warningmark
+
+Aggregate mode does not work in this build.
+
+**Function**
+
+Finds overlap between two data sets, narrowed by given parameter.
+
+This tool is still in deveopment.
+
+  </help>
+  <outputs>
+    <data format="tabular" name="output1" label="0-1 Bucket" from_work_dir="bucket_0-1.txt" />
+    <data format="tabular" name="output2" label="1-0 Bucket" from_work_dir="bucket_1-0.txt" />
+    <data format="tabular" name="output3" label="1-1 Bucket" from_work_dir="bucket_1-1.txt" />
+    <data format="tabular" name="output4" label="1-n Bucket" from_work_dir="bucket_1-n.txt" />
+    <data format="tabular" name="output5" label="n-1 Bucket" from_work_dir="bucket_n-1.txt" />
+  	<data format="tabular" name="output6" label="n-m Bucket" from_work_dir="bucket_n-m.txt" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="fa_gc_content_input.fa"/>
+      <output name="out_file1" file="fa_gc_content_output.txt"/>
+    </test>
+  </tests>
+
+</tool>
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