changeset 29:c78966712a57

Deleted selected files

--- a/SMART/galaxy/test.py	Mon Apr 29 03:31:52 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,97 +0,0 @@
-#! /usr/bin/env python
-
-import os
-import sys
-import getopt
-from commons.core.checker.CheckerException import CheckerException
-
-SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"]
-
-class WrappGetLetterDistribution(object):
-    
-    def __init__(self):
-        self._inputFileName = ""
-        self._inputFileFormat = ""
-        self._outputFileName = "tmpOutputFile"
-        self._csv = False
-
-    def help( self ):
-        print 
-        print "usage: %s [ options ]" % ( sys.argv[0] )
-        print "options:"
-        print "     -h: this help"
-        print "     -i: input file"
-        print "     -f: 'fasta' or 'fastq'"
-        print "     -c: CSV output file"
-        print "     -a: first PNG output file"
-        print "     -b: second PNG output file"
-        print
-        print "Exemple:"
-        print
-        print "1:\n\tpython WrappGetLetterDistribution.py -i inputFile.fasta -f fasta -c outputFile1.csv -a outputFile2.png -b outputFile3.png"
-        print
-        print "2:\n\tpython WrappGetLetterDistribution.py -i inputFile.fastq -f fastq -c outputFile1.csv -a outputFile2.png -b outputFile3.png"
-        print
-        print
-
-
-    def setAttributesFromCommandLine(self):
-        try:
-            opts, args = getopt.getopt( sys.argv[1:], "hi:f:a:b:c:" )
-        except getopt.GetoptError, err:
-            print str(err); sys.exit(1)
-        for o, a in opts:
-            if o == "-h":
-                self.help()
-                sys.exit(0)
-            if o == "-i":
-                self._inputFileName = a
-            elif o == "-f":
-                self._inputFileFormat = a
-            elif o == "-c":             
-                self._outputFileNameCSV = a  
-                self._csv = True
-            elif o == "-a":
-                self._outputFileNamePNG = a
-            elif o == "-b":
-                self._outputFileNamePerNtPNG = a 
-
-    def checkAttributes(self):
-        lMsg = []
-        if self._inputFileName == "" and not os.path.exists(self._inputFileName):
-            lMsg.append("ERROR: This input file doesn't exist!")
-        if self._inputFileFormat == "":
-            lMsg.append("ERROR: No input file format specified in option!")
-        if self._outputFileNamePNG == "":
-            lMsg.append("ERROR: No output file.png specified in option!")            
-        if self._outputFileNamePerNtPNG == "":
-            lMsg.append("ERROR: No output filePerNt.png specified in option!")
-        if self._outputFileNameCSV == "" and self._csv == True :
-            lMsg.append("ERROR: No output file.csv specified in option!")   
-            
-        print ">>> lMsg " + str(lMsg)
-        if lMsg != []:
-            exp = CheckerException()
-            exp.setMessages(lMsg)
-            raise (exp)
-
-    def _cleanWorkingDir(self, cDir):
-        os.system("rm %s/tmpData* %s/tmpScript*" % (cDir, cDir))
-        
-    def wrapp(self):
-        self.checkAttributes()
-	cDir = os.getcwd()
-
-        if self._csv == True:
-            os.system("python %s/Java/Python/getLetterDistribution.py -i %s -f %s -o %s/%s -c" % (SMART_PATH, self._inputFileName, self._inputFileFormat, cDir, self._outputFileName))
-            os.system("mv %s/%s.csv %s" % (cDir, self._outputFileName, self._outputFileNameCSV))
-            os.system("mv %s/%s.png %s" % (cDir, self._outputFileName, self._outputFileNamePNG))
-            os.system("mv %s/%sPerNt.png %s" % (cDir, self._outputFileName, self._outputFileNamePerNtPNG))
-
-        self._cleanWorkingDir(cDir)
-
-if __name__ == '__main__':
-    launcher = WrappGetLetterDistribution()
-    launcher.setAttributesFromCommandLine()
-    launcher.wrapp()
-

--- a/SMART/galaxy/test.xml	Mon Apr 29 03:31:52 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<tool id="test" name="test">
-	<description>This is a test.</description>
-    <requirements>
-        <requirement type="set_environment">PYTHONPATH</requirement>
-    </requirements>
-	<requirement type="package" version="1.0">R_PACKAGES</requirement>
-	<command>env > $outputFile; R --slave --no-save --no-restore --quiet -e 'rownames(installed.packages())' >> $outputFile</command>
-	<outputs>
-		<data name="outputFile" format="txt" label="output test file"/>
-	</outputs> 
-    <help>This is a test.</help>	
-</tool>