To whom it may concern,
Greetings. My current work to wrap a tool for galaxy. The function of this tool is to analyze the WGBS result (call methylation, compare difference in methylation between target genome and reference genome, etc.).
I can run first part of the tool in unix like this: $ func1 -m 001.bam -r /data/hg19.fa --fullMode 0 -m means mapped .bam/.sam files, -r means reference genome, --fullMode 0 means do not open full mode. func1 is an exec file.
The result would be 3 files: 001.bam.G.bed, 001.bam.HG.bed, and 001.bam_stat.txt.
How should I edit the XML file to fit in this tool? What should I write in <command> section?
Thank you so much.