comparison picard_MarkDuplicatesWithMateCigar.xml @ 21:6f9c0884a3e7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 78c3dea7dcd0c854fe7e6dc1d2b2349956167661

20:2a17c789e0a5

    REMOVE_DUPLICATES="${remove_duplicates}"
    ASSUME_SORTED="${assume_sorted}"

    DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"

    #import pipes
    READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" }
    OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"


    BLOCK_SIZE=100000
    VALIDATION_STRINGENCY="${validation_stringency}"

      <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
    </param>


    <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
      <sanitizer>
        <valid initial="string.printable">
        </valid>
      </sanitizer>
    </param>
    <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>

   <expand macro="VS" />

21:6f9c0884a3e7

    REMOVE_DUPLICATES="${remove_duplicates}"
    ASSUME_SORTED="${assume_sorted}"

    DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"

    READ_NAME_REGEX='${ str( $read_name_regex ) }'
    OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"


    BLOCK_SIZE=100000
    VALIDATION_STRINGENCY="${validation_stringency}"

      <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>
    </param>


    <param name="read_name_regex" type="text" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">
      <expand macro="sanitize_query" />
    </param>
    <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>

   <expand macro="VS" />