comments

[bernt-matthias]

It would be an option to have the data in a Galaxt data table (.loc file etc) directory. In particular if there are multiple possible models available. Then we could also remove the reference to __tool_data_directory__

cfm-galaxy/tools/cfm/cfmid.xml

Line 8 in 9f20359

#set $tool_directory = $getVar('__tool_directory__', '../../../../tools/cfm')

Also allow users to update their own models could be nice.

I think that a for details of the python script should be documented in the help section: eg

cfm-galaxy/tools/cfm/cfmid.py

Line 50 in 9f20359

mz2 = mz-1.007276

or

cfm-galaxy/tools/cfm/cfmid.py

Line 65 in 9f20359

if (t[0] > mz_ranges[0]) and (t[0] < mz_ranges[1]):

You should check the return code of this

cfm-galaxy/tools/cfm/cfmid.py

Line 94 in 9f20359

os.system(cmd_command)

Does one call of the python script maybe generate multiple calls to cfm-id. I'm just guessing here. Could allow for some paralellization, eg on Galaxy side.