Metaphlan2 to use paired-end reads

Allow usage of Metaphlan2 with paired-end data.

Also bit a cleaning in the repo.

Closes #14 (closed)

tools/metaphlan2/metaphlan2/paired/Snakefile

+__metaphlan2_exec_command = config.get('metaphlan2', {}).get('exec_command', 'metaphlan2.py')
+__metaphlan2_modules = config.get('metaphlan2', {}).get('modules')
+__metaphlan2_input_type = config['metaphlan2'].get('input_type', 'fastq')
+__metaphlan2_options = config.get('metaphlan2', {}).get('options', "")
+__metaphlan2_threads = config.get('metaphlan2', {}).get('threads', 1)
+
+
+rule metaphlan2_paired:
+    """
+    MetaPhlAn 2 can also natively handle paired-end metagenomes (but does not use the paired-end information),
+    and, more generally, metagenomes stored in multiple files (but you need to specify the --bowtie2out parameter):
+
+    $ metaphlan2.py metagenome_1.fastq,metagenome_2.fastq --bowtie2out metagenome.bowtie2.bz2 --nproc 5 
+                    --input_type fastq > profiled_metagenome.txt
+
+    """
+    input:
+        r1 = __metaphlan2_input_r1,
+        r2 = __metaphlan2_input_r2
+    output:
+        __metaphlan2_output
+    params:
+        exec_command = __metaphlan2_exec_command,
+        modules = __metaphlan2_modules,
+        input_type = __metaphlan2_input_type,
+        bowtie2out = "{output_dir}/{sample}.bowtie2.bz2".format(output_dir=__metaphlan2_output_dir, sample="{sample}"),
+        options = __metaphlan2_options
+    threads:
+        __metaphlan2_threads
+    run:
+        command = []
+        if params.modules:
+            command.append("module load {params.modules}")
+        command.append("{params.exec_command} --nproc {threads} --input_type {params.input_type} --bowtie2out {params.bowtie2out} {params.options} {input.r1},{input.r2} {output}")
+        shell(" && ".join(command))