I am trying to create tools for Automatic Image Registration (AIR) package. Initially, I developed python script which calls align_warp, reslice and softmean tools from AIR package. My problem is when I test my tool with planemo, these tools don’t get some related data files. The command line for align_warp tool is as follows:
align_warp anatomy.img reference.img output.warp -m 12
Along with the files in the command line, align_warp also needs anatomy.hdr and reference.hdr header files which must reside in the same directory as anatomy.img and reference.img.
The problem is when I run test with Planemo, the anatomy.img and reference.img are copied in a temp directory with different names. Even if I add anatomy.hdr and reference.hdr as input parameters, align_warp doesn’t find them because they were renamed.
planemo t align_warp.xml
What I need is Galaxy should copy these files to a temp directory without renaming them and without removing their extensions.
Can anyone please help me with this?
Galaxy related questions are best asked over at their help forum: https://help.galaxyproject.org/
Thanks. I already tried over there, got no answers in 2 days. I have at least got one reply here.