"""
import logging
import optparse
+import os
import sys
from htsworkflow.pipelines import runfolder
runs = []
if opt.run_xml:
+ # handle ~ shortcut
+ opt.run_xml = os.path.expanduser(opt.run_xml)
tree = ElementTree.parse(opt.run_xml).getroot()
runs.append(runfolder.PipelineRun(xml=tree))
for run_dir in args: