Mercurial > repos > yufei-luo > s_mart

changeset 21:91f8c4ce8c27

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Deleted selected files
author m-zytnicki
date Mon, 29 Apr 2013 03:25:37 -0400
parents c265f13066d8
children 1e3f2c2657a3
files SMART/galaxy/test/CollapseReads.xml SMART/galaxy/test/Test_F_WrappGetLetterDistribution.py SMART/galaxy/test/__init__.py
diffstat 2 files changed, 0 insertions(+), 140 deletions(-) [+]
line wrap: on
line diff
--- a/SMART/galaxy/test/CollapseReads.xml	Mon Apr 29 03:24:43 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- 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
@@ -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