--- a/BlastParser_and_hits.py	Fri Jun 19 13:17:32 2015 -0400
+++ b/BlastParser_and_hits.py	Mon Jun 29 06:06:11 2015 -0400
@@ -14,6 +14,9 @@
     the_parser.add_argument('--tabularOutput', action="store", type=str, help="tabular output file of blast analysis")
     the_parser.add_argument('--flanking', action="store", type=int, help="number of flanking nucleotides added to the hit sequences") 
     the_parser.add_argument('--mode', action="store", choices=["verbose", "short"], type=str, help="reporting (verbose) or not reporting (short) oases contigs")
+    the_parser.add_argument('--filter_relativeCov', action="store", type=float, default=0, help="filter out relative coverages below the specified ratio (float number)")
+    the_parser.add_argument('--filter_maxScore', action="store", type=float, default=0, help="filter out maximum BitScore below the specified float number")
+    the_parser.add_argument('--filter_meanScore', action="store", type=float, default=0, help="filter out maximum BitScore below the specified float number")
     args = the_parser.parse_args()
     if not all ( (args.sequences, args.blast, args.fastaOutput, args.tabularOutput) ):
         the_parser.error('argument(s) missing, call the -h option of the script')
@@ -122,12 +125,14 @@
         leftCoordinate = 1
     return getseq (fastadict, FastaHeader, leftCoordinate, rightCoordinate, polarity)
     
-def outputParsing (F, Fasta, results, Xblastdict, fastadict, mode="verbose"):
+def outputParsing (F, Fasta, results, Xblastdict, fastadict, filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, mode="verbose"):
     F= open(F, "w")
     Fasta=open(Fasta, "w")
     if mode == "verbose":
         print >>F, "# SeqId\t%Identity\tAlignLength\tStartSubject\tEndSubject\t%QueryHitCov\tE-value\tBitScore\n"
         for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
+            if results[subject]["RelativeSubjectCoverage"]<filter_relativeCov or results[subject]["maxBitScores"]<filter_maxScore or results[subject]["meanBitScores"]<filter_meanScore:
+                continue
             print >> F, "#\n# %s" % subject
             print >> F, "# Suject Length: %s" % (results[subject]["subjectLength"])
             print >> F, "# Total Subject Coverage: %s" % (results[subject]["TotalCoverage"])
@@ -149,6 +154,8 @@
     else:
         print >>F, "# subject\tsubject length\tTotal Subject Coverage\tRelative Subject Coverage\tMaximum Bit Score\tMean Bit Score"
         for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
+            if results[subject]["RelativeSubjectCoverage"]<filter_relativeCov or results[subject]["maxBitScores"]<filter_maxScore or results[subject]["meanBitScores"]<filter_meanScore:
+                continue
             line = []
             line.append(subject)
             line.append(results[subject]["subjectLength"])
@@ -173,5 +180,7 @@
     results = defaultdict(dict)
     for subject in Xblastdict:
         results[subject]["HitDic"], results[subject]["subjectLength"], results[subject]["TotalCoverage"], results[subject]["RelativeSubjectCoverage"], results[subject]["maxBitScores"], results[subject]["meanBitScores"]  = subjectCoverage(fastadict, Xblastdict, subject, args.flanking)
-    outputParsing (args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict, args.mode)
+    outputParsing (args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict,
+                  filter_relativeCov=args.filter_relativeCov, filter_maxScore=args.filter_maxScore,
+                  filter_meanScore=args.filter_meanScore, mode=args.mode)
 if __name__=="__main__": __main__()

--- a/BlastParser_and_hits.xml	Fri Jun 19 13:17:32 2015 -0400
+++ b/BlastParser_and_hits.xml	Mon Jun 29 06:06:11 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.1.0">
+<tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.2.0">
 <description>for virus discovery</description>
 <requirements></requirements>
 <command interpreter="python">
@@ -9,6 +9,13 @@
 	--fastaOutput $fastaOutput
 	--flanking $flanking
 	--mode $mode
+	## Additional parameters.
+    #if $additional_filters.use_filters == "yes":
+        --filter_relativeCov $additional_filters.filter_relativeCov
+        --filter_maxScore $additional_filters.filter_maxScore
+        --filter_meanScore $additional_filters.filter_meanScore
+    #end if
+
 </command>
 <inputs>
 	<param name="sequences" type="data" format="fasta"  label="fasta sequences that have been blasted" />
@@ -18,6 +25,19 @@
 	    <option value="verbose" default="true">verbose</option>
 	    <option value="short">do not report oases contigs</option>
 	</param>
+    <conditional name="additional_filters">
+            <param name="use_filters" type="select" label="Use Additional Filters?">
+                <option value="no">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no">
+            </when>
+            <when value="yes">            
+                <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
+                <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
+                <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
+            </when>
+    </conditional>
 </inputs>
 <outputs>
 	<data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>