comparison grinder.xml @ 7:bac7e652a9aa

Added mate orientation option

6:68576b1d2d8b

      #if str($read_dist):
        -read_dist        $read_dist
      #end if
      #if str($insert_dist):
        -insert_dist      $insert_dist
      #end if
      #if str($exclude_chars):
        -exclude_chars    $exclude_chars
      #end if
      #if str($delete_chars):

    <param name="insert_dist" type="text" value="0" optional="true" label="Insert size distribution" help="Create shotgun paired end reads (mate pairs) spanning the given insert length (the reads are interior to the insert):
   0 : off,
   or: insert size distribution in bp, in the same format as the read length
       distribution (a typical value is 2,500 bp)
Two distinct reads are generated whether or not the mate pair overlaps.
Default: insert_dist.default" />

    <param name="exclude_chars" type="text" optional="true" label="Characters to exclude" help="Do not create reads containing any of the specified characters (case insensitive), e.g. 'N-' to prevent reads with gaps (-) or ambiguities (N)." />

    <param name="delete_chars" type="text" optional="true" label="Characters to delete" help="Remove the specified characters from the reference sequences (case insensitive), e.g. 'N-' to remove gaps (-) and ambiguities (N)." />

7:bac7e652a9aa

      #if str($read_dist):
        -read_dist        $read_dist
      #end if
      #if str($insert_dist):
        -insert_dist      $insert_dist
      #end if
      #if str($mate_orientation):
        -mate_orientation $mate_orientation
      #end if
      #if str($exclude_chars):
        -exclude_chars    $exclude_chars
      #end if
      #if str($delete_chars):

    <param name="insert_dist" type="text" value="0" optional="true" label="Insert size distribution" help="Create shotgun paired end reads (mate pairs) spanning the given insert length (the reads are interior to the insert):
   0 : off,
   or: insert size distribution in bp, in the same format as the read length
       distribution (a typical value is 2,500 bp)
Two distinct reads are generated whether or not the mate pair overlaps." />

    <param name="mate_orientation" type="text" value="FR" optional="true" label="Mate orientation" help="When generating paired-end or mate-pair reads (see the insert distribution parameter), specify the orientation of the reads (F: forward, R: reverse): FR for Sanger or Illumina paired-end, FF for 454, RF for Illumina mate-pairs, or RR" />

    <param name="exclude_chars" type="text" optional="true" label="Characters to exclude" help="Do not create reads containing any of the specified characters (case insensitive), e.g. 'N-' to prevent reads with gaps (-) or ambiguities (N)." />

    <param name="delete_chars" type="text" optional="true" label="Characters to delete" help="Remove the specified characters from the reference sequences (case insensitive), e.g. 'N-' to remove gaps (-) and ambiguities (N)." />