Metaphlan2 to use paired-end reads

tools/README.md

tools/metaphlan2/metaphlan2/paired/Snakefile

tools/metaphlan2/metaphlan2/paired/config_example.yaml

tools/metaphlan2/metaphlan2/single/Snakefile

tools/metaphlan2/metaphlan2/single/config_example.yaml

tools/metaphlan2/metaphlan2/usage_example.rules

workflows/README.md

workflows/metaphlan2/README.md

workflows/metaphlan2/paired_metaphlan2/Snakefile

workflows/metaphlan2/paired_metaphlan2/config.yaml

workflows/metaphlan2/single_metaphlan2/Snakefile

workflows/metaphlan2/single_metaphlan2/config.yaml

workflows/simple_metaphlan2/README.md

workflows/simple_metaphlan2/config.yaml