| Previous changeset 20:c265f13066d8 (2013-04-29) Next changeset 22:1e3f2c2657a3 (2013-04-29) |
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Commit message:
Deleted selected files |
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removed:
SMART/galaxy/test/CollapseReads.xml SMART/galaxy/test/Test_F_WrappGetLetterDistribution.py SMART/galaxy/test/__init__.py |
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| diff -r c265f13066d8 -r 91f8c4ce8c27 SMART/galaxy/test/CollapseReads.xml --- a/SMART/galaxy/test/CollapseReads.xml Mon Apr 29 03:24:43 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,49 +0,0 @@ -<tool id="collapseReads" name="collapseReads"> - <description>Merges two reads if they have exactly the same genomic coordinates.</description> - <command interpreter="python"> - ../Java/Python/CollapseReads.py -i $formatType.inputFileName - #if $formatType.FormatInputFileName == 'bed': - -f bed - #elif $formatType.FormatInputFileName == 'gff': - -f gff - #elif $formatType.FormatInputFileName == 'gff2': - -f gff2 - #elif $formatType.FormatInputFileName == 'gff3': - -f gff3 - #end if - - -$strand - -o $outputFileGff - --galaxy - </command> - - <inputs> - <conditional name="formatType"> - <param name="FormatInputFileName" type="select" label="Input File Format"> - <option value="bed">bed</option> - <option value="gff">gff</option> - <option value="gff2">gff2</option> - <option value="gff3">gff3</option> - </param> - <when value="bed"> - <param name="inputFileName" format="bed" type="data" label="Input File"/> - </when> - <when value="gff"> - <param name="inputFileName" format="gff" type="data" label="Input File"/> - </when> - <when value="gff2"> - <param name="inputFileName" format="gff2" type="data" label="Input File"/> - </when> - <when value="gff3"> - <param name="inputFileName" format="gff3" type="data" label="Input File"/> - </when> - </conditional> - - <param name="strand" type="boolean" truevalue="-s" falsevalue="" checked="false" label="Strand option merges 2 different strands[default:False]."/> - </inputs> - - <outputs> - <data name="outputFileGff" format="gff3"/> - </outputs> - -</tool> \ No newline at end of file |
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| diff -r c265f13066d8 -r 91f8c4ce8c27 SMART/galaxy/test/Test_F_WrappGetLetterDistribution.py --- a/SMART/galaxy/test/Test_F_WrappGetLetterDistribution.py Mon Apr 29 03:24:43 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,91 +0,0 @@ -import unittest -import os -from commons.core.utils.FileUtils import FileUtils -from SMART.galaxy.WrappGetLetterDistribution import WrappGetLetterDistribution - -SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"] -SMART_DATA = SMART_PATH + "/data" - -class Test_F_WrappGetLetterDistribution(unittest.TestCase): - - - def setUp(self): - self._dirTest = "%s/galaxy/test" % SMART_PATH - self._iwrappFastq = WrappGetLetterDistribution() - self._iwrappFasta = WrappGetLetterDistribution() - self._expOutputCSV = "expOutputTomate.csv" - - def test_wrappFasta(self): - self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA - self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH - self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH - self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH - self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH - self._iwrappFasta._inputFileFormat = "fasta" - self._iwrappFasta._csv = True - if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)): - self._iwrappFasta.wrapp() - self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG)) - self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG)) - self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNameCSV)) - self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFasta._outputFileNameCSV,self._expOutputCSV)) - else: - print "Problem : the input fasta file %s is empty!" % self._inputFileFasta - - -# def test_wrappFasta_withoutCSV_Opt(self): -# self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA -# self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH -# self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH -# self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH -# self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH -# self._iwrappFasta._inputFileFormat = "fasta" -# self._iwrappFasta._csv = False -# if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)): -# self._iwrappFasta.wrapp() -# self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG)) -# self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG)) -# else: -# print "Problem : the input fasta file %s is empty!" % self._inputFileFasta -# os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH) -# os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH) -# -# -# def test_wrappFastq(self): -# self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA -# self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH -# self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH -# self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH -# self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH -# self._iwrappFastq._inputFileFormat = "fastq" -# self._iwrappFastq._csv = True -# if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)): -# self._iwrappFastq.wrapp() -# self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG)) -# self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG)) -# self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNameCSV)) -# self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFastq._outputFileNameCSV,self._expOutputCSV)) -# else: -# print "Problem : the input fastq file %s is empty!" % self._inputFileFastq -# -# -# def test_wrappFastq_withoutCSV_Opt(self): -# self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA -# self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH -# self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH -# self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH -# self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH -# self._iwrappFastq._inputFileFormat = "fastq" -# self._iwrappFastq._csv = False -# if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)): -# self._iwrappFastq.wrapp() -# self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG)) -# self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG)) -# else: -# print "Problem : the input fastq file %s is empty!" % self._inputFileFastq -# os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH) -# os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH) - - -if __name__ == "__main__": - unittest.main() \ No newline at end of file |