add sample2markers for strainphlan

tools/strainphlan/sample2markers/README.md

+# sample2markers.py for strainphlan
+
+This step will reconstruct all species strains found in metaphlan output sam file and store them in a pickle file (*.pkl). Those strains are referred as sample-reconstructed strains.
+
+### Help section
+
+```
+usage: sample2markers.py [-h] [-i INPUT [INPUT ...]] [--sorted]
+                         [-f INPUT_FORMAT] [-o OUTPUT_DIR]
+                         [-b BREADTH_THRESHOLD] [-n NPROCS]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -i INPUT [INPUT ...], --input INPUT [INPUT ...]
+                        The input samples as SAM or BAM files
+  --sorted              Whether the BAM input files are sorted. Default false
+  -f INPUT_FORMAT, --input_format INPUT_FORMAT
+                        The input samples format {bam, sam, bz2}. Default bz2
+  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
+                        The output directory
+  -b BREADTH_THRESHOLD, --breadth_threshold BREADTH_THRESHOLD
+                        The breadth of coverage threshold for the consensus
+                        markers. Default 80 (%)
+  -n NPROCS, --nprocs NPROCS
+                        The number of threads to execute the script
+```

tools/strainphlan/sample2markers/Snakefile

+__sample2markers_exec_command = config.get('sample2markers', {}).get('exec_command', 'sample2markers.py')
+__sample2markers_modules = config.get('sample2markers', {}).get('modules')
+__sample2markers_options = config.get('sample2markers', {}).get('options', "")
+__sample2markers_threads = config.get('sample2markers', {}).get('threads', 1)
+
+
+rule sample2markers:
+    input:
+        __sample2markers_input
+    output:
+        dir = __sample2markers_output_dir,
+        file = __sample2markers_output
+    params:
+        exec_command = __sample2markers_exec_command,
+        modules = __sample2markers_modules,
+        options = __sample2markers_options
+    threads:
+        __sample2markers_threads
+    run:
+        command = []
+        if params.modules:
+            command.append("module load {params.modules}")
+        command.append("{params.exec_command} -n {threads} {params.options} -i {input} -o {output.dir}")
+        shell(" && ".join(command))

tools/strainphlan/sample2markers/config.yaml

+input_dir: data
+
+sample2markers:
+  threads: 1
+  exec_command: sample2markers.py