add SnakeFile for metaphlan2 merge

tools/metaphlan2/metaphlan2/config.yaml

@@ -3,5 +3,5 @@ input_dir: data
 metaphlan2:
   threads: 1
   input_type: fastq
-  options: "COMMAND LINE OPTIONS"
+  options: ""
   exec_command: metaphlan2.py

tools/metaphlan2/metaphlan2_merge/config.yaml

+samples:
+  - S1
+  - S2
+input_dir: data
+
+metaphlan2_merge:
+  options: ""
+  exec_command: merge_metaphlan_tables.py
\ No newline at end of file

tools/metaphlan2/metaphlan2_merge/metaphlan2_merge.rules

+__metaphlan2_merge_exec_command = config['metaphlan2_merge'].get('exec_command', 'merge_metaphlan_tables.py')
+__metaphlan2_merge_options = config['metaphlan2_merge'].get('options', "")
+
+rule metaphlan2_merge:
+    input:
+        __metaphlan2_merge_input
+    output:
+        __metaphlan2_merge_output
+    params:
+        exec_command = __metaphlan2_merge_exec_command,
+        options = __metaphlan2_merge_options
+    shell:
+        "{params.exec_command} {params.options} {input} > {output}"

tools/metaphlan2/metaphlan2_merge/usage_example.rules

+"""
+This example would be used as followed:
+
+$ snakemake --snakefile metaphlan2_merge.rules
+
+It requires the presence of input files within data to work based on config file
+	e.g. : data/S1.txt
+	       data/S2.txt
+"""
+
+configfile: "config.yaml"
+
+__input_dir = config['input_dir']
+__main_output_dir = config.get('output_dir', 'output')
+
+# ---- Metaphlan2 merge
+__metaphlan2_merge_output_dir = __main_output_dir + "/metaphlan2_merge"
+__metaphlan2_merge_output_file_name = config['metaphlan2_merge'].get('output_file_name',"merged_taxonomic_profiles.txt")
+__metaphlan2_merge_input = expand("{dir}/{sample}.txt".format(dir=__input_dir,
+                                                              sample="{sample}"),
+                                  sample=config['samples'])
+__metaphlan2_merge_output = "{dir}/{file_name}".format(dir=__metaphlan2_merge_output_dir,
+                                                       file_name=__metaphlan2_merge_output_file_name) 
+include: "metaphlan2_merge.rules"
+
+rule all:
+    input:
+        __metaphlan2_merge_output