comparison picard_MarkDuplicates.xml @ 16:d837223d4ad2 draft

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

15:a5a13ea16d17

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

    DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'

    #import pipes
    #if $read_name_regex:
      READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) }
    #end if
    OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'

    # Optional arguments
    #if $barcode_tag:

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

    <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard 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='' (uses : separation)">

      <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"/>

    <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices."/>

16:d837223d4ad2

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

    DUPLICATE_SCORING_STRATEGY='${duplicate_scoring_strategy}'

    #if $read_name_regex:
      READ_NAME_REGEX='${ str( $read_name_regex ) }'
    #end if
    OPTICAL_DUPLICATE_PIXEL_DISTANCE='${optical_duplicate_pixel_distance}'

    # Optional arguments
    #if $barcode_tag:

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

    <param name="read_name_regex" type="text" value="" label="Regular expression that can be used in unusual situations to parse non-standard 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='' (uses : separation)">
      <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"/>

    <param name="barcode_tag" type="text" optional="True" label="Barcode Tag" help="Barcode SAM tag. This tag can be utilized when you have data from an assay that includes Unique Molecular Indices."/>