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Viewing changes to source/TEST/TOPP/SEARCHENGINES/CMakeLists.txt

  • Committer: Package Import Robot
  • Author(s): Filippo Rusconi
  • Date: 2013-12-20 11:30:16 UTC
  • mfrom: (5.1.2 sid)
  • Revision ID: package-import@ubuntu.com-20131220113016-wre5g9bteeheq6he
Tags: 1.11.1-3
* remove version number from libbost development package names;
* ensure that AUTHORS is correctly shipped in all packages.

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source/TEST/TOPP/SEARCHENGINES/CMakeLists.txt
 
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## optional tests. Configured in OpenMS/cmake/OpenMSBuildSystem_testConfig.cmake
 
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if (NOT (${OMSSA_BINARY} STREQUAL "OMSSA_BINARY-NOTFOUND"))
 
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  add_test("TOPP_OMSSAAdapter_1" ${TOPP_BIN_PATH}/OMSSAAdapter -test -ini ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1.ini -database ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1.fasta -in ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1.mzML -out OMSSAAdapter_1_out.tmp -omssa_executable "${OMSSA_BINARY}")
 
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  add_test("TOPP_OMSSAAdapter_1_out" ${DIFF} -in1 OMSSAAdapter_1_out.tmp -in2 ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1_out.idXML -whitelist "IdentificationRun date" "SearchParameters id=\"SP_0\" db=")
 
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  set_tests_properties("TOPP_OMSSAAdapter_1_out" PROPERTIES DEPENDS "TOPP_OMSSAAdapter_1")
 
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endif()
 
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if (NOT (${XTANDEM_BINARY} STREQUAL "XTANDEM_BINARY-NOTFOUND"))
 
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  add_test("TOPP_XTandemAdapter_1" ${TOPP_BIN_PATH}/XTandemAdapter -test -ini ${DATA_DIR_TOPP}/SEARCHENGINES/XTandemAdapter_1.ini -database ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1.fasta -in ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1.mzML -out XTandemAdapter_1_out.tmp -xtandem_executable "${XTANDEM_BINARY}")
 
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  add_test("TOPP_XTandemAdapter_1_out" ${DIFF} -in1 XTandemAdapter_1_out.tmp -in2 ${DATA_DIR_TOPP}/SEARCHENGINES/XTandemAdapter_1_out.idXML -whitelist "IdentificationRun date" "SearchParameters id=\"SP_0\" db=")
 
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  set_tests_properties("TOPP_XTandemAdapter_1_out" PROPERTIES DEPENDS "TOPP_XTandemAdapter_1")
 
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endif()
 
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if (NOT (${MYRIMATCH_BINARY} STREQUAL "MYRIMATCH_BINARY-NOTFOUND"))
 
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  add_test("TOPP_MyriMatchAdapter_1" ${TOPP_BIN_PATH}/MyriMatchAdapter -test -ini ${DATA_DIR_TOPP}/SEARCHENGINES/MyriMatchAdapter_1.ini -database ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1.fasta -in ${DATA_DIR_TOPP}/SEARCHENGINES/OMSSAAdapter_1.mzML -out MyriMatchAdapter_1_out.tmp -myrimatch_executable "${MYRIMATCH_BINARY}")
 
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  add_test("TOPP_MyriMatchAdapter_1_out" ${DIFF} -in1 MyriMatchAdapter_1_out.tmp -in2 ${DATA_DIR_TOPP}/SEARCHENGINES/MyriMatchAdapter_1_out.idXML -whitelist "IdentificationRun date" "SearchParameters id=\"SP_0\" db=")
 
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  set_tests_properties("TOPP_MyriMatchAdapter_1_out" PROPERTIES DEPENDS "TOPP_MyriMatchAdapter_1")
 
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endif()
 
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# TODO the following tests are waiting for better implementations of InspectAdapter and associated classes
 
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#add_test("TOPP_InspectAdapter_3" ${TOPP_BIN_PATH}/InspectAdapter -ini ${DATA_DIR_TOPP}/InspectAdapter_1_parameters.ini -trie_dbs ${DATA_DIR_TOPP}/Inspect_FASTAFile_test2.trie -in ${DATA_DIR_TOPP}/InspectAdapter.out -dbs ${DATA_DIR_TOPP}/Inspect_FASTAFile_test.fasta -out InspectAdapter_4_output.tmp -inspect_out)
 
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#add_test("TOPP_InspectAdapter_3_out1" ${DIFF} -whitelist "?xml-stylesheet" "IdentificationRun date" -in1 InspectAdapter_4_output.tmp -in2 ${DATA_DIR_TOPP}/InspectAdapter_4_output.idXML )
 
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#set_tests_properties("TOPP_InspectAdapter_3_out1" PROPERTIES DEPENDS "TOPP_InspectAdapter_3")
 
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### SequestAdapter tests
 
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# TODO disabled until tool is reactivated
 
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#add_test("TOPP_SequestAdapter_1" ${TOPP_BIN_PATH}/SequestAdapter -ini ${DATA_DIR_TOPP}/SequestAdapter_1_parameters.ini -in ${DATA_DIR_TOPP}/Sequest.mzXML -mz_files ${DATA_DIR_TOPP}/Sequest.mzXML -modifications_xml_file ${DATA_DIR_TOPP}/Sequest_PTMs.xml -out SequestAdapter_2_output.tmp -sequest_in -temp_data_directory ${DATA_DIR_TOPP} -db ${DATA_DIR_TOPP}/Sequest_FASTAFile_test.fasta)
 
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#add_test("TOPP_SequestAdapter_1_out1" ${DIFF} -in1 SequestAdapter_2_output.tmp -in2 ${DATA_DIR_TOPP}/SequestAdapter_2_output.sequest_in)
 
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#add_test("TOPP_SequestAdapter_2" ${TOPP_BIN_PATH}/SequestAdapter -ini ${DATA_DIR_TOPP}/SequestAdapter_1_parameters.ini -in ${DATA_DIR_TOPP}/Sequest.mzData -mz_files ${DATA_DIR_TOPP}/Sequest.mzXML -modifications_xml_file ${DATA_DIR_TOPP}/Sequest_PTMs.xml -out SequestAdapter_3_output.tmp -sequest_in -temp_data_directory ${DATA_DIR_TOPP} -db ${DATA_DIR_TOPP}/Sequest_FASTAFile_test.fasta)
 
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#add_test("TOPP_SequestAdapter_2_out1" ${DIFF} -in1 SequestAdapter_3_output.tmp -in2 ${DATA_DIR_TOPP}/SequestAdapter_2_output.sequest_in)
 
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# TODO the following tests are waiting for better implementations of InspectAdapter and
 
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# associated classes
 
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#add_test("TOPP_SequestAdapter_3" ${TOPP_BIN_PATH}/SequestAdapter -ini ${DATA_DIR_TOPP}/SequestAdapter_2_parameters.ini -mz_files ${DATA_DIR_TOPP}/Sequest.mzXML -modifications_xml_file ${DATA_DIR_TOPP}/Sequest_PTMs.xml -in ${DATA_DIR_TOPP}/Sequest.mzXML -out SequestAdapter_4_output.tmp -temp_data_directory ${DATA_DIR_TOPP} -db ${DATA_DIR_TOPP}/Sequest_FASTAFile_test.fasta)
 
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#add_test("TOPP_SequestAdapter_3_out1" ${DIFF} -in1 SequestAdapter_4_output.tmp -in2 ${DATA_DIR_TOPP}/SequestAdapter_4_output.idXML)
 
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### SpecLibSearcher tests
 
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#add_test("TOPP_SpecLibSearcher_1" ${TOPP_BIN_PATH}/SpecLibSearcher -test -ini ${DATA_DIR_TOPP}/SpecLibSearcher_1_parameters.ini -in ${DATA_DIR_TOPP}/SpecLibSearcher_1.MzData -lib $(DATA_DIR_TOPP)/SpecLibSearcher_1.MSP -out SpecLibSearcher_1.tmp)
 
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#add_test("TOPP_SpecLibSearcher_1_out1" ${DIFF} -in1 SpecLibSearcher_1.tmp  -in2 $(DATA_DIR_TOPP)/SpecLibSearcher_1.idXML)
 
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### PepNovoAdapter tests
 
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#The PepNovoAdapter now only works as a frontend and cannot be run without an installation of PepNovo.Therefore no test possible
 
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#add_test("TOPP_PepNovoAdapter_1" ${TOPP_BIN_PATH}/PepNovoAdapter -ini ${DATA_DIR_TOPP}/PepNovoAdapter_1_parameters.ini -in ${DATA_DIR_TOPP}/PepNovo.mzXML -pepnovo_in -out PepNovoAdapter_3_output.tmp -dta_list ${DATA_DIR_TOPP}/tmp/dta_list.txt -model_directory ${DATA_DIR_TOPP}/tmp/ -temp_data_directory ${DATA_DIR_TOPP}/tmp/)
 
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#add_test("TOPP_PepNovoAdapter_1_out1" ${DIFF} -in1 ${DATA_DIR_TOPP}/tmp/PepNovo_PTMs_.txt -in2 ${DATA_DIR_TOPP}/tmp/PepNovo_PTMs.txt)
 
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#TODO ANDREAS - We have to clean up the /tmp/ directory to run this test multiple times
 
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#add_test("TOPP_PepNovoAdapter_2" ${TOPP_BIN_PATH}/PepNovoAdapter -ini ${DATA_DIR_TOPP}/PepNovoAdapter_1_parameters.ini -in ${DATA_DIR_TOPP}/PepNovo.mzData -pepnovo_in -out PepNovoAdapter_4_output.tmp -temp_data_directory ${DATA_DIR_TOPP})
 
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#add_test("TOPP_PepNovoAdapter_2_out1" ${DIFF} -in1 ${DATA_DIR_TOPP}/PepNovo_PTMs_.txt -in2 ${DATA_DIR_TOPP}/PepNovo_PTMs.txt)
 
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#add_test("TOPP_PepNovoAdapter_3" ${TOPP_BIN_PATH}/PepNovoAdapter -ini ${DATA_DIR_TOPP}/PepNovoAdapter_5_parameters.ini -in ${DATA_DIR_TOPP}/PepNovoAdapter_5_output.pepnovo_out -out PepNovoAdapter_5_output.tmp -pepnovo_out -dta_list ${DATA_DIR_TOPP}/tmp/dta_list.txt -model_directory ${DATA_DIR_TOPP}/tmp/ -temp_data_directory ${DATA_DIR_TOPP}/tmp/ -modifications_xml_file ${DATA_DIR_TOPP}/PepNovo_PTMs.xml -mz_files ${DATA_DIR_TOPP}/PepNovo.mzXML)
 
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#add_test("TOPP_PepNovoAdapter_3_out1" ${DIFF} -whitelist "?xml-stylesheet" "date_group_1" -in1 PepNovoAdapter_5_output.tmp -in2 ${DATA_DIR_TOPP}/PepNovoAdapter_5_output.idXML)
 
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