################################################################################
##
## Copyright (c) 2007-2011 Illumina, Inc.
##
## This software is covered by the "Illumina Genome Analyzer Software
## License Agreement" and the "Illumina Source Code License Agreement",
## and certain third party copyright/licenses, and any user of this
## source file is bound by the terms therein (see accompanying files
## Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
## Illumina_Source_Code_License_Agreement.pdf and third party
## copyright/license notices).
##
## This file is part of the Consensus Assessment of Sequence And VAriation
## (CASAVA) software package.
##
## file ProjectSummary.mk
##
## brief Partial makefile to build the Summary.{xml,xsl,htm} file for the whole flow cell.
##
## Detailed description comes here.
##
## author Roman Petrovski
##
################################################################################

.PRECIOUS: $($(project)_OUT_DIR)/Sample_Summary.htm $($(project)_OUT_DIR)/Barcode_Lane_Summary.htm

include $(MAKEFILES_DIR)/ProjectThumbnails.mk

$($(project)_SUMMARY_DIR)/Sample_Summary.htm: project:=$(project)
$($(project)_SUMMARY_DIR)/Sample_Summary.htm: $($(project)_SUMMARY_DIR)/.sentinel \
  $($(project)_SUMMARY_DIR)/$(SCORE_XML) $($(project)_SUMMARY_DIR)/$(RESCORE_XML) \
  $($(project)_SAMPLE_PAIR_XML_FILES) config.xml \
  $(EXPT_DIR)/DemultiplexedBustardSummary.xml $(TEMP_DIR)/SampleSheet.xml \
  css/Reports.css \
  $($(project)_SUMMARY_$(PEC_THUMB)_TARGET) $($(project)_SUMMARY_$(MISMATCH_THUMB)_TARGET)
	$(CMDPREFIX) $(XSLTPROC) \
	--stringparam IVC_PLOT_PARAM '$(EXPT_DIR)/Basecall_Stats_$(FLOWCELL)/IVC.htm' \
	--stringparam ALL_PLOT_PARAM '$(EXPT_DIR)/Basecall_Stats_$(FLOWCELL)/All.htm' \
	--stringparam PEC_PLOT_PARAM '$(notdir $($(project)_SUMMARY_$(PEC_THUMB)_TARGET))' \
	--stringparam MISMATCH_PLOT_PARAM '$(notdir $($(project)_SUMMARY_$(MISMATCH_THUMB)_TARGET))' \
	--stringparam PROJECT_PATH_PARAM '$(CURDIR)/$($(project)_SUMMARY_DIR)' \
	--stringparam PROJECT_NAME_PARAM '$(project)' \
	--stringparam SAMPLE_SHEET_PATH_PARAM $(CURDIR)/$(TEMP_DIR)/SampleSheet.xml \
	--stringparam BUSTARD_SUMMARY_PATH_PARAM '$(EXPT_DIR)/DemultiplexedBustardSummary.xml' \
	--stringparam SCORE_XML_PARAM '$(CURDIR)/$($(project)_SUMMARY_DIR)/$(SCORE_XML)' \
	--stringparam RESCORE_XML_PARAM '$(CURDIR)/$($(project)_SUMMARY_DIR)/$(RESCORE_XML)' \
	--stringparam FLOWCELL_PARAM '$(FLOWCELL)' \
	$(DATA_DIR)/ProjectSampleSummary.xsl config.xml > $(SAFEPIPETARGET)

$($(project)_SUMMARY_DIR)/Barcode_Lane_Summary.htm: project:=$(project)
$($(project)_SUMMARY_DIR)/Barcode_Lane_Summary.htm: $($(project)_SUMMARY_DIR)/.sentinel \
  $($(project)_SUMMARY_DIR)/$(SCORE_XML) $($(project)_SUMMARY_DIR)/$(RESCORE_XML) \
  $($(project)_DATASET_PAIR_XML_FILES) config.xml \
  $(EXPT_DIR)/DemultiplexedBustardSummary.xml $(TEMP_DIR)/SampleSheet.xml \
  css/Reports.css \
  $($(project)_SUMMARY_$(PEC_THUMB)_TARGET) $($(project)_SUMMARY_$(MISMATCH_THUMB)_TARGET)
	$(CMDPREFIX) $(XSLTPROC) \
	--stringparam IVC_PLOT_PARAM '$(EXPT_DIR)/Basecall_Stats_$(FLOWCELL)/IVC.htm' \
	--stringparam ALL_PLOT_PARAM '$(EXPT_DIR)/Basecall_Stats_$(FLOWCELL)/All.htm' \
	--stringparam PEC_PLOT_PARAM '$(notdir $($(project)_SUMMARY_$(PEC_THUMB)_TARGET))' \
	--stringparam MISMATCH_PLOT_PARAM '$(notdir $($(project)_SUMMARY_$(MISMATCH_THUMB)_TARGET))' \
	--stringparam PROJECT_PATH_PARAM '$(CURDIR)/$($(project)_SUMMARY_DIR)' \
	--stringparam PROJECT_NAME_PARAM '$(project)' \
	--stringparam SAMPLE_SHEET_PATH_PARAM '$(CURDIR)/$(TEMP_DIR)/SampleSheet.xml' \
	--stringparam BUSTARD_SUMMARY_PATH_PARAM '$(EXPT_DIR)/DemultiplexedBustardSummary.xml' \
	--stringparam SCORE_XML_PARAM '$(CURDIR)/$($(project)_SUMMARY_DIR)/$(SCORE_XML)' \
	--stringparam RESCORE_XML_PARAM '$(CURDIR)/$($(project)_SUMMARY_DIR)/$(RESCORE_XML)' \
	--stringparam FLOWCELL_PARAM '$(FLOWCELL)' \
	$(DATA_DIR)/ProjectBarcodeLaneSummary.xsl config.xml > $(SAFEPIPETARGET)

$($(project)_SUMMARY_DIR)/$(SCORE_XML): \
  $($(project)_SUMMARY_DIR)/.sentinel \
  $($(project)_SCORE_FILES)
	$(CMDPREFIX) $(ECHO) '<?xml version="1.0"?><Stats/>' $(foreach part_summ, $($(project)_SCORE_FILES), \
		| $(XSLTPROC) --stringparam with $(part_summ) $(DATA_DIR)/MergeXmlDocuments.xsl -) \
	> $(SAFEPIPETARGET)

$($(project)_SUMMARY_DIR)/$(RESCORE_XML): \
  $($(project)_SUMMARY_DIR)/.sentinel \
  $($(project)_RESCORE_FILES)
	$(CMDPREFIX) $(ECHO) '<?xml version="1.0"?><Stats/>' $(foreach part_summ, $($(project)_RESCORE_FILES), \
		| $(XSLTPROC) --stringparam with $(part_summ) $(DATA_DIR)/MergeXmlDocuments.xsl -) \
	> $(SAFEPIPETARGET)


DATASET_TARGETS += $($(project)_SUMMARY_DIR)/Sample_Summary.htm $($(project)_SUMMARY_DIR)/Barcode_Lane_Summary.htm