| Previous changeset 59:2a4884ba3e5c (2014-02-10) Next changeset 61:3a52eb875640 (2014-02-21) |
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Commit message:
Uploaded |
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modified:
SMART/Java/Python/CompareOverlappingSmallRef.py SMART/Java/Python/clusterize.py SMART/galaxy/Clusterize.xml SMART/galaxy/CompareOverlappingAdapt.xml SMART/galaxy/CompareOverlappingSmallQuery.xml SMART/galaxy/CompareOverlappingSmallRef.xml |
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added:
SMART/Java/Python/misc/RPlotter.pyc SMART/Java/Python/structure/TranscriptContainer.pyc SMART/galaxy/.CompareOverlappingSmallRef.xml.swp |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/Java/Python/CompareOverlappingSmallRef.py --- a/SMART/Java/Python/CompareOverlappingSmallRef.py Mon Feb 10 03:39:09 2014 -0500 +++ b/SMART/Java/Python/CompareOverlappingSmallRef.py Fri Feb 21 08:32:36 2014 -0500 |
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| @@ -235,6 +235,7 @@ cosr.includeNotOverlapping(options.notOverlapping) cosr.setDistance(options.distance) cosr.setAntisense(options.antisense) + cosr.setCollinear(options.collinear) cosr.setInvert(options.exclude) cosr.setMinPercentOverlap(options.pcOverlapQuery, options.pcOverlapRef) cosr.setMinOverlap(options.minOverlap) |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/Java/Python/clusterize.py --- a/SMART/Java/Python/clusterize.py Mon Feb 10 03:39:09 2014 -0500 +++ b/SMART/Java/Python/clusterize.py Fri Feb 21 08:32:36 2014 -0500 |
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| b'@@ -33,6 +33,7 @@\n \n import os, os.path, random\n from optparse import OptionParser\n+from heapq import heappush, heappop\n from commons.core.parsing.ParserChooser import ParserChooser\n from commons.core.writer.Gff3Writer import Gff3Writer\n from SMART.Java.Python.structure.Transcript import Transcript\n@@ -44,26 +45,31 @@\n class Clusterize(object):\n \n \tdef __init__(self, verbosity):\n-\t\tself.normalize\t\t = False\n-\t\tself.presorted\t\t = False\n-\t\tself.distance\t\t = 1\n-\t\tself.colinear\t\t = False\n-\t\tself.nbWritten\t\t = 0\n-\t\tself.nbMerges\t\t = 0\n-\t\tself.verbosity\t\t = verbosity\n+\t\tself.parsers = {}\n+\t\tself.sortedFileNames = {}\n+\t\tself.normalize = False\n+\t\tself.presorted = False\n+\t\tself.distance = 1\n+\t\tself.collinear = False\n+\t\tself.nbWritten = 0\n+\t\tself.nbMerges = 0\n+\t\tself.verbosity = verbosity\n \t\tself.splittedFileNames = {}\n+\t\tself.chromosomes = set()\n \n \tdef __del__(self):\n-\t\tfor fileName in self.splittedFileNames.values():\n-\t\t\tos.remove(fileName)\n+\t\tfor fileName1 in self.splittedFileNames:\n+\t\t\tfor fileName2 in self.splittedFileNames[fileName1].values():\n+\t\t\t\tos.remove(fileName2)\n \n-\tdef setInputFile(self, fileName, format):\n+\tdef setInputFiles(self, fileNames, format):\n \t\tparserChooser = ParserChooser(self.verbosity)\n \t\tparserChooser.findFormat(format)\n-\t\tself.parser = parserChooser.getParser(fileName)\n-\t\tself.sortedFileName = "%s_sorted_%d.pkl" % (os.path.splitext(fileName)[0], random.randint(1, 100000))\n-\t\tif "SMARTTMPPATH" in os.environ:\n-\t\t\tself.sortedFileName = os.path.join(os.environ["SMARTTMPPATH"], os.path.basename(self.sortedFileName))\n+\t\tfor fileName in fileNames:\n+\t\t\tself.parsers[fileName] = parserChooser.getParser(fileName)\n+\t\t\tself.sortedFileNames[fileName] = "%s_sorted_%d.pkl" % (os.path.splitext(fileName)[0], random.randint(1, 100000))\n+\t\t\tif "SMARTTMPPATH" in os.environ:\n+\t\t\t\tself.sortedFileNames[fileName] = os.path.join(os.environ["SMARTTMPPATH"], os.path.basename(self.sortedFileNames[fileName]))\n \n \tdef setOutputFileName(self, fileName, format="gff3", title="S-MART", feature="transcript", featurePart="exon"):\n \t\twriterChooser = WriterChooser()\n@@ -76,8 +82,8 @@\n \tdef setDistance(self, distance):\n \t\tself.distance = distance\n \n-\tdef setColinear(self, colinear):\n-\t\tself.colinear = colinear\n+\tdef setColinear(self, collinear):\n+\t\tself.collinear = collinear\n \n \tdef setNormalize(self, normalize):\n \t\tself.normalize = normalize\n@@ -85,42 +91,60 @@\n \tdef setPresorted(self, presorted):\n \t\tself.presorted = presorted\n \n-\tdef _sortFile(self):\n+\tdef _sortFiles(self):\n \t\tif self.presorted:\n \t\t\treturn\n-\t\tfs = FileSorter(self.parser, self.verbosity-4)\n-\t\tfs.perChromosome(True)\n-\t\tfs.setPresorted(self.presorted)\n-\t\tfs.setOutputFileName(self.sortedFileName)\n-\t\tfs.sort()\n-\t\tself.splittedFileNames = fs.getOutputFileNames()\n-\t\tself.nbElementsPerChromosome = fs.getNbElementsPerChromosome()\n-\t\tself.nbElements = fs.getNbElements()\n+\t\tfor fileName, parser in self.parsers.iteritems():\n+\t\t\tfs = FileSorter(parser, self.verbosity-4)\n+\t\t\tfs.perChromosome(True)\n+\t\t\tfs.setPresorted(self.presorted)\n+\t\t\tfs.setOutputFileName(self.sortedFileNames[fileName])\n+\t\t\tfs.sort()\n+\t\t\tself.splittedFileNames[fileName] = fs.getOutputFileNames()\n+\t\t\tself.nbElementsPerChromosome = fs.getNbElementsPerChromosome()\n+\t\t\tself.nbElements = fs.getNbElements()\n+\t\t\tself.chromosomes.update(self.splittedFileNames[fileName].keys())\n \t\t\n-\tdef _iterate(self, chromosome):\n-\t\tif chromosome == None:\n-\t\t\tprogress = UnlimitedProgress(10000, "Reading input file", self.verbosity)\n-\t\t\tparser = self.parser\n-\t\telse:\n-\t\t\tprogress = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)\n-\t\t\tparser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)\n+\tdef _iterate(self):\n+\t\tprogress = UnlimitedProgress(10000, "Reading input file", self.verbosity)\n \t\ttranscripts = []\n-\t\tfor newTranscript in parser.getIterat'..b'+\t\tself._iterate()\n \t\tself.writer.close()\n \t\tif self.verbosity > 0:\n \t\t\tprint "# input: %d" % (self.nbElements)\n@@ -162,21 +182,21 @@\n \tdescription = "Clusterize v1.0.3: clusterize the data which overlap. [Category: Merge]"\n \n \tparser = OptionParser(description = description)\n-\tparser.add_option("-i", "--input", dest="inputFileName", action="store",\t\t\t\t type="string", help="input file [compulsory] [format: file in transcript format given by -f]")\n-\tparser.add_option("-f", "--format", dest="format",\t\t action="store",\t\t\t\t type="string", help="format of file [format: transcript file format]")\n-\tparser.add_option("-o", "--output", dest="outputFileName", action="store",\t\t\t\t type="string", help="output file [compulsory] [format: output file in transcript format given by -u]")\n-\tparser.add_option("-u", "--outputFormat", dest="outputFormat", action="store", default="gff",\t\t type="string", help="output file format [format: transcript file format]")\n-\tparser.add_option("-c", "--colinear", dest="colinear", action="store_true", default=False,\t\t\t\thelp="merge colinear transcripts only [format: bool] [default: false]")\n-\tparser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="max. distance between two transcripts to be merged [format: int] [default: 0]")\n-\tparser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False,\t\t\t\thelp="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")\n-\tparser.add_option("-s", "--sorted", dest="sorted",\t\t action="store_true", default=False,\t\t\t\thelp="input is already sorted [format: bool] [default: false]")\n-\tparser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")\n+\tparser.add_option("-i", "--inputs", dest="inputFileNames", action="store",\t\t\t\t type="string", help="input files (separated by commas) [compulsory] [format: string]")\n+\tparser.add_option("-f", "--format", dest="format",\t\t action="store",\t\t\t\t type="string", help="format of file [format: transcript file format]")\n+\tparser.add_option("-o", "--output", dest="outputFileName", action="store",\t\t\t\t type="string", help="output file [compulsory] [format: output file in transcript format given by -u]")\n+\tparser.add_option("-u", "--outputFormat", dest="outputFormat", action="store", default="gff",\t\t type="string", help="output file format [format: transcript file format]")\n+\tparser.add_option("-c", "--collinear", dest="collinear", action="store_true", default=False,\t\t\t\thelp="merge collinear transcripts only [format: bool] [default: false]")\n+\tparser.add_option("-d", "--distance", dest="distance", action="store", default=0, type="int", help="max. distance between two transcripts to be merged [format: int] [default: 0]")\n+\tparser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False,\t\t\t\thelp="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")\n+\tparser.add_option("-s", "--sorted", dest="sorted",\t\t action="store_true", default=False,\t\t\t\thelp="input is already sorted [format: bool] [default: false]")\n+\tparser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")\n \t(options, args) = parser.parse_args()\n \n \tc = Clusterize(options.verbosity)\n-\tc.setInputFile(options.inputFileName, options.format)\n+\tc.setInputFiles(options.inputFileNames.split(","), options.format)\n \tc.setOutputFileName(options.outputFileName, options.outputFormat)\n-\tc.setColinear(options.colinear)\n+\tc.setColinear(options.collinear)\n \tc.setDistance(options.distance)\n \tc.setNormalize(options.normalize)\n \tc.setPresorted(options.sorted)\n' |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/Java/Python/misc/RPlotter.pyc |
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| Binary file SMART/Java/Python/misc/RPlotter.pyc has changed |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/Java/Python/structure/TranscriptContainer.pyc |
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| Binary file SMART/Java/Python/structure/TranscriptContainer.pyc has changed |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/galaxy/.CompareOverlappingSmallRef.xml.swp |
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| Binary file SMART/galaxy/.CompareOverlappingSmallRef.xml.swp has changed |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/galaxy/Clusterize.xml --- a/SMART/galaxy/Clusterize.xml Mon Feb 10 03:39:09 2014 -0500 +++ b/SMART/galaxy/Clusterize.xml Fri Feb 21 08:32:36 2014 -0500 |
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| @@ -4,26 +4,8 @@ <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> - ../Java/Python/clusterize.py -i $formatType.inputFileName - #if $formatType.FormatInputFileName == 'bed': - -f bed - #elif $formatType.FormatInputFileName == 'gff': - -f gff - #elif $formatType.FormatInputFileName == 'gff2': - -f gff2 - #elif $formatType.FormatInputFileName == 'gff3': - -f gff3 - #elif $formatType.FormatInputFileName == 'sam': - -f sam - #elif $formatType.FormatInputFileName == 'bam': - -f bam - #elif $formatType.FormatInputFileName == 'gtf': - -f gtf - #end if - -o $outputFileGff - $colinear - $normalize - -d $distance + #set $inputFiles = ",".join(["%s" % (s) for s in $formatType.inputFileName]) + ../Java/Python/clusterize.py -i $inputFiles -f $formatType.FormatInputFileName -o $outputFileGff $colinear $normalize -d $distance </command> <inputs> @@ -34,29 +16,29 @@ <option value="gff2">gff2</option> <option value="gff3">gff3</option> <option value="sam">sam</option> + <option value="gtf">gtf</option> <option value="bam">bam</option> - <option value="gtf">gtf</option> </param> <when value="bed"> - <param name="inputFileName" format="bed" type="data" label="Input File"/> + <param name="inputFileName" format="bed" type="data" multiple="true" label="Input File"/> </when> <when value="gff"> - <param name="inputFileName" format="gff" type="data" label="Input File"/> + <param name="inputFileName" format="gff" type="data" multiple="true" label="Input File"/> </when> <when value="gff2"> - <param name="inputFileName" format="gff2" type="data" label="Input File"/> + <param name="inputFileName" format="gff2" type="data" multiple="true" label="Input File"/> </when> <when value="gff3"> - <param name="inputFileName" format="gff3" type="data" label="Input File"/> + <param name="inputFileName" format="gff3" type="data" multiple="true" label="Input File"/> </when> <when value="sam"> - <param name="inputFileName" format="sam" type="data" label="Input File"/> + <param name="inputFileName" format="sam" type="data" multiple="true" label="Input File"/> + </when> + <when value="gtf"> + <param name="inputFileName" format="gtf" type="data" multiple="true" label="Input File"/> </when> <when value="bam"> - <param name="inputFileName" format="bam" type="data" label="Input File"/> - </when> - <when value="gtf"> - <param name="inputFileName" format="gtf" type="data" label="Input File"/> + <param name="inputFileName" format="bam" type="data" multiple="true" label="Input File"/> </when> </conditional> |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/galaxy/CompareOverlappingAdapt.xml --- a/SMART/galaxy/CompareOverlappingAdapt.xml Mon Feb 10 03:39:09 2014 -0500 +++ b/SMART/galaxy/CompareOverlappingAdapt.xml Fri Feb 21 08:32:36 2014 -0500 |
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| @@ -4,45 +4,15 @@ <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> - ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1 - #if $formatType.FormatInputFileName1 == 'bed': - -f bed - #elif $formatType.FormatInputFileName1 == 'gff': - -f gff - #elif $formatType.FormatInputFileName1 == 'gff2': - -f gff2 - #elif $formatType.FormatInputFileName1 == 'gff3': - -f gff3 - #elif $formatType.FormatInputFileName1 == 'sam': - -f sam - #elif $formatType.FormatInputFileName1 == 'gtf': - -f gtf - #end if - -j $formatType2.inputFileName2 - #if $formatType2.FormatInputFileName2 == 'bed': - -g bed - #elif $formatType2.FormatInputFileName2 == 'gff': - -g gff - #elif $formatType2.FormatInputFileName2 == 'gff2': - -g gff2 - #elif $formatType2.FormatInputFileName2 == 'gff3': - -g gff3 - #elif $formatType2.FormatInputFileName2 == 'sam': - -g sam - #elif $formatType2.FormatInputFileName2 == 'gtf': - -g gtf - #end if - -o $outputFileGff + ../Java/Python/CompareOverlappingAdapt.py -i $formatType.inputFileName1 -f $formatType.FormatInputFileName1 -j $formatType2.inputFileName2 -g $formatType2.FormatInputFileName2 -o $outputFileGff $InvertMatch $NotOverlapping -m $NbOverlap #if $OptionDistance.Dist == 'Yes': -d $OptionDistance.distance #end if - #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': + #if $OptionCA == 'Collinear': -c - #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': + #elif $OptionCA == 'AntiSense': -a #end if - $InvertMatch - $NotOverlapping </command> <inputs> @@ -114,21 +84,14 @@ <when value="No"> </when> </conditional> - <conditional name="OptionCollinearOrAntiSens"> - <param name="OptionCA" type="select" label="Collinear or anti-sens"> - <option value="Collinear">Collinear</option> - <option value="AntiSens">AntiSens</option> - <option value="NONE" selected="true">NONE</option> - </param> - <when value="Collinear"> - </when> - <when value="AntiSens"> - </when> - <when value="NONE"> - </when> - </conditional> + <param name="OptionCA" type="select" label="Collinear or anti-sense features only"> + <option value="Collinear">Collinear</option> + <option value="AntiSense">AntiSense</option> + <option value="All" selected="true">All</option> + </param> <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/> <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/> + <param name="NbOverlap" type="integer" value="1" label="Min. # of overlapping nt. to declare an overlap."/> </inputs> <outputs> |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/galaxy/CompareOverlappingSmallQuery.xml --- a/SMART/galaxy/CompareOverlappingSmallQuery.xml Mon Feb 10 03:39:09 2014 -0500 +++ b/SMART/galaxy/CompareOverlappingSmallQuery.xml Fri Feb 21 08:32:36 2014 -0500 |
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| @@ -4,60 +4,21 @@ <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> - ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1 - #if $formatType.FormatInputFileName1 == 'bed': - -f bed - #elif $formatType.FormatInputFileName1 == 'gff': - -f gff - #elif $formatType.FormatInputFileName1 == 'gff2': - -f gff2 - #elif $formatType.FormatInputFileName1 == 'gff3': - -f gff3 - #elif $formatType.FormatInputFileName1 == 'sam': - -f sam - #elif $formatType.FormatInputFileName1 == 'bam': - -f bam - #elif $formatType.FormatInputFileName1 == 'gtf': - -f gtf - #end if - -j $formatType2.inputFileName2 - #if $formatType2.FormatInputFileName2 == 'bed': - -g bed - #elif $formatType2.FormatInputFileName2 == 'gff': - -g gff - #elif $formatType2.FormatInputFileName2 == 'gff2': - -g gff2 - #elif $formatType2.FormatInputFileName2 == 'gff3': - -g gff3 - #elif $formatType2.FormatInputFileName2 == 'sam': - -g sam - #elif $formatType2.FormatInputFileName2 == 'bam': - -g bam - #elif $formatType2.FormatInputFileName2 == 'gtf': - -g gtf - #end if - -o $outputFileGff + ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1 -f $formatType.FormatInputFileName1 -j $formatType2.inputFileName2 -g $formatType2.FormatInputFileName2 -o $outputFileGff $InvertMatch $NotOverlapping $OptionInclusionQuery $OptionInclusionRef -m $OptionMinOverlap #if $OptionDistance.Dist == 'Yes': -d $OptionDistance.distance #end if - #if $OptionMinOverlap.present == 'Yes': - -m $OptionMinOverlap.minOverlap - #end if #if $OptionPcOverlapQuery.present == 'Yes': -p $OptionPcOverlapQuery.minOverlap #end if #if $OptionPcOverlapRef.present == 'Yes': -P $OptionPcOverlapRef.minOverlap #end if - #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': + #if $OptionCA == 'Collinear': -c - #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': + #elif $OptionCA == 'AntiSense': -a #end if - $InvertMatch - $NotOverlapping - $OptionInclusionQuery - $OptionInclusionRef </command> <inputs> @@ -91,7 +52,7 @@ </when> <when value="gtf"> <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> - </when> + </when> </conditional> <conditional name="formatType2"> @@ -137,24 +98,14 @@ <when value="No"> </when> </conditional> - <conditional name="OptionMinOverlap"> - <param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> - </when> - <when value="No"> - </when> - </conditional> + <param name="OptionMinOverlap" type="integer" value="1" label="Min. # of overlapping nt. to declare an overlap."/> <conditional name="OptionPcOverlapQuery"> <param name="present" type="select" label="N% of the query must overlap"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> + <param name="minOverlap" type="integer" value="100"/> </when> <when value="No"> </when> @@ -165,26 +116,18 @@ <option value="No" selected="true">No</option> </param> <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> + <param name="minOverlap" type="integer" value="100"/> </when> <when value="No"> </when> </conditional> - <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a query"/> + <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a reference"/> <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must be nested in a query"/> - <conditional name="OptionCollinearOrAntiSens"> - <param name="OptionCA" type="select" label="Collinear or anti-sens"> - <option value="Collinear">Collinear</option> - <option value="AntiSens">AntiSens</option> - <option value="NONE" selected="true">NONE</option> - </param> - <when value="Collinear"> - </when> - <when value="AntiSens"> - </when> - <when value="NONE"> - </when> - </conditional> + <param name="OptionCA" type="select" label="Collinear or anti-sense only"> + <option value="Collinear">Collinear</option> + <option value="AntiSense">AntiSense</option> + <option value="All" selected="true">All</option> + </param> <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/> <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/> </inputs> |
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| diff -r 2a4884ba3e5c -r 90f4b29d884f SMART/galaxy/CompareOverlappingSmallRef.xml --- a/SMART/galaxy/CompareOverlappingSmallRef.xml Mon Feb 10 03:39:09 2014 -0500 +++ b/SMART/galaxy/CompareOverlappingSmallRef.xml Fri Feb 21 08:32:36 2014 -0500 |
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| @@ -1,63 +1,24 @@ <tool id="CompareOverlappingSmallRef" name="compare overlapping small reference"> - <description>Provide the queries that overlap with a reference, when the reference dataset is small.</description> + <description>Provide the queries that overlap with a reference, when the query data set is small.</description> <requirements> <requirement type="set_environment">PYTHONPATH</requirement> </requirements> <command interpreter="python"> - ../Java/Python/CompareOverlappingSmallQuery.py -i $formatType.inputFileName1 - #if $formatType.FormatInputFileName1 == 'bed': - -f bed - #elif $formatType.FormatInputFileName1 == 'gff': - -f gff - #elif $formatType.FormatInputFileName1 == 'gff2': - -f gff2 - #elif $formatType.FormatInputFileName1 == 'gff3': - -f gff3 - #elif $formatType.FormatInputFileName1 == 'sam': - -f sam - #elif $formatType.FormatInputFileName1 == 'bam': - -f bam - #elif $formatType.FormatInputFileName1 == 'gtf': - -f gtf - #end if - -j $formatType2.inputFileName2 - #if $formatType2.FormatInputFileName2 == 'bed': - -g bed - #elif $formatType2.FormatInputFileName2 == 'gff': - -g gff - #elif $formatType2.FormatInputFileName2 == 'gff2': - -g gff2 - #elif $formatType2.FormatInputFileName2 == 'gff3': - -g gff3 - #elif $formatType2.FormatInputFileName2 == 'sam': - -g sam - #elif $formatType2.FormatInputFileName2 == 'bam': - -g bam - #elif $formatType2.FormatInputFileName2 == 'gtf': - -g gtf - #end if - -o $outputFileGff + ../Java/Python/CompareOverlappingSmallRef.py -i $formatType.inputFileName1 -f $formatType.FormatInputFileName1 -j $formatType2.inputFileName2 -g $formatType2.FormatInputFileName2 -o $outputFileGff $InvertMatch $NotOverlapping $OptionInclusionQuery $OptionInclusionRef -m $OptionMinOverlap #if $OptionDistance.Dist == 'Yes': -d $OptionDistance.distance #end if - #if $OptionMinOverlap.present == 'Yes': - -m $OptionMinOverlap.minOverlap - #end if #if $OptionPcOverlapQuery.present == 'Yes': -p $OptionPcOverlapQuery.minOverlap #end if #if $OptionPcOverlapRef.present == 'Yes': -P $OptionPcOverlapRef.minOverlap #end if - #if $OptionCollinearOrAntiSens.OptionCA == 'Collinear': + #if $OptionCA == 'Collinear': -c - #elif $OptionCollinearOrAntiSens.OptionCA == 'AntiSens': + #elif $OptionCA == 'AntiSense': -a #end if - $InvertMatch - $NotOverlapping - $OptionInclusionQuery - $OptionInclusionRef </command> <inputs> @@ -91,7 +52,7 @@ </when> <when value="gtf"> <param name="inputFileName1" format="gtf" type="data" label="Input File 1"/> - </when> + </when> </conditional> <conditional name="formatType2"> @@ -137,24 +98,14 @@ <when value="No"> </when> </conditional> - <conditional name="OptionMinOverlap"> - <param name="present" type="select" label="Minimum number of common nucleotides to declare an overlap"> - <option value="Yes">Yes</option> - <option value="No" selected="true">No</option> - </param> - <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> - </when> - <when value="No"> - </when> - </conditional> + <param name="OptionMinOverlap" type="integer" value="1" label="Min. # of overlapping nt. to declare an overlap."/> <conditional name="OptionPcOverlapQuery"> <param name="present" type="select" label="N% of the query must overlap"> <option value="Yes">Yes</option> <option value="No" selected="true">No</option> </param> <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> + <param name="minOverlap" type="integer" value="100"/> </when> <when value="No"> </when> @@ -165,26 +116,18 @@ <option value="No" selected="true">No</option> </param> <when value="Yes"> - <param name="minOverlap" type="integer" value="0"/> + <param name="minOverlap" type="integer" value="100"/> </when> <when value="No"> </when> </conditional> - <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a query"/> + <param name="OptionInclusionQuery" type="boolean" truevalue="-k" falsevalue="" checked="false" label="The query must be nested in a reference"/> <param name="OptionInclusionRef" type="boolean" truevalue="-K" falsevalue="" checked="false" label="The reference must be nested in a query"/> - <conditional name="OptionCollinearOrAntiSens"> - <param name="OptionCA" type="select" label="Collinear or anti-sens"> - <option value="Collinear">Collinear</option> - <option value="AntiSens">AntiSens</option> - <option value="NONE" selected="true">NONE</option> - </param> - <when value="Collinear"> - </when> - <when value="AntiSens"> - </when> - <when value="NONE"> - </when> - </conditional> + <param name="OptionCA" type="select" label="Collinear or anti-sense only"> + <option value="Collinear">Collinear</option> + <option value="AntiSense">AntiSense</option> + <option value="All" selected="true">All</option> + </param> <param name="InvertMatch" type="boolean" truevalue="-x" falsevalue="" checked="false" label="Invert match: the output file will contain all query elements which do NOT overlap"/> <param name="NotOverlapping" type="boolean" truevalue="-O" falsevalue="" checked="false" label="Also report the query data which do not overlap, with the nbOverlaps tag set to 0."/> </inputs> |