add rule and example for metaphlan2

tools/metaphlan2/metaphlan2/config.yaml

+input_dir: data
+
+metaphlan2:
+  threads: 1
+  input_type: fastq
+  options: "COMMAND LINE OPTIONS"
+  exec_command: metaphlan2.py

tools/metaphlan2/metaphlan2/metaphlan2.rules

+__metaphlan2_exec_command = config['metaphlan2'].get('exec_command', 'metaphlan2.py')
+__metaphlan2_options = config['metaphlan2'].get('options', "")
+__metaphlan2_threads = config['metaphlan2'].get('threads', 1)
+
+rule metaphlan2:
+    input:
+        __metaphlan2_input
+    output:
+        __metaphlan2_output
+    params:
+        exec_command = __metaphlan2_exec_command,
+        input_type = __metaphlan2_input_type,
+        options = __metaphlan2_options
+    threads:
+        __metaphlan2_threads
+    shell:
+        "{params.exec_command} --nproc {threads} --input_type {params.input_type} {params.options} {input} {output}"

tools/metaphlan2/metaphlan2/usage_example.rules

+"""
+This example would be used as followed:
+
+$ snakemake --snakefile metaphlan2.rules output/s01.txt 
+
+It requires the presence of data/s01.fastq.gz to work based on config file
+"""
+
+configfile: "config.yaml"
+
+__input_dir = config['input_dir']
+__main_output_dir = config.get('output_dir', 'output')
+
+# ---- Metaphlan2
+__metaphlan2_output_dir = __main_output_dir + "/metaphlan2"
+__metaphlan2_input_type = config['metaphlan2'].get('input_type', 'fastq')
+__metaphlan2_input = "{dir}/{sample}.{ext}".format(dir=__input_dir,
+                                                   sample="{sample}",
+                                                   ext=__metaphlan2_input_type + ".gz")
+__metaphlan2_output = "{dir}/{sample}.txt".format(dir=__metaphlan2_output_dir,
+                                                  sample="{sample}")
+include: "metaphlan2.rules"
+
+rule all:
+    input:
+        __metaphlan2_output