Attention: not currently compatible with the latest CWL draft. This is a work in progress.
TODO: generate a two-step workflow (1st step runs cheetah to get the command line, 2nd step runs actual tool
Auto convert Galaxy tool XML to CWL Draft-2 CommandLineTool.
May be used as a command line tool:
$ ./galaxy2cwl.py bwa/bwa-mem.xml
Wrote bwa/bwa-mem.cwl
May also be imported as a module:
import galaxy2cwl
import xml.dom.minidom
galaxy2cwl.galaxy2cwl(xml.dom.minidom.parse("bwa/bwa-mem.xml").documentElement, "bwa")