| Previous changeset 28:2a3fdec156e0 (2013-04-29) Next changeset 30:5677346472b5 (2013-04-29) |
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Commit message:
Deleted selected files |
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removed:
SMART/galaxy/test.py SMART/galaxy/test.xml |
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| diff -r 2a3fdec156e0 -r c78966712a57 SMART/galaxy/test.py --- a/SMART/galaxy/test.py Mon Apr 29 03:31:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 "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 "Exemple:" - print "1:\n\tpython WrappGetLetterDistribution.py -i inputFile.fasta -f fasta -c outputFile1.csv -a outputFile2.png -b outputFile3.png" - print "2:\n\tpython WrappGetLetterDistribution.py -i inputFile.fastq -f fastq -c outputFile1.csv -a outputFile2.png -b outputFile3.png" - - - 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() - |
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| diff -r 2a3fdec156e0 -r c78966712a57 SMART/galaxy/test.xml --- a/SMART/galaxy/test.xml Mon Apr 29 03:31:52 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |