RTPredict: fixed order of parameters and doc

new interface gives 'svm_model' and 'total_gradient_time' in one block with other input options, and not below the output block (which tends to confuse people at lot).
After this fix:

Usage:
  RTPredict <options>

Options (mandatory options marked with '*'):
  -in_id <file>                Peptides with precursor information (valid formats: 'idXML')
  -in_text <file>              Peptides as text-based file (valid formats: 'txt')
  -svm_model <file>*           Svm model in libsvm format (can be produced by RTModel) (valid formats: 'txt')
  -total_gradient_time <time>  The time (in seconds) of the gradient (peptide RT prediction) (default: '1' min: '1e-005')

Output files in idXML format:
...