comparison picard_MarkDuplicates.xml @ 12:a459ead5ab75 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6

11:3d8d70436d02

<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.0">
  <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />

    @symlink_element_identifier@
    picard
    MarkDuplicates

    INPUT='$escaped_element_identifier'
    OUTPUT="${outFile}"

    METRICS_FILE="${metrics_file}"
    #for $element in $comments:
      COMMENT="${element.comment}"
    #end for
    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}"

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR

  ]]></command>
  <inputs>

        <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" />

  </inputs>

                                The maximum offset between two duplicte clusters in order to consider them optical
                                duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
                                unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
                                which case 50-100 is more normal.  Default value: 100.

@more_info@

  </help>
</tool>

12:a459ead5ab75

<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.1">
  <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />

    @symlink_element_identifier@
    picard
    MarkDuplicates

    INPUT='$escaped_element_identifier'
    OUTPUT='${outFile}'

    METRICS_FILE='${metrics_file}'
    #for $element in $comments:
      COMMENT='${element.comment}'
    #end for

    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}'

    # Optional arguments
    #if $barcode_tag:
    BARCODE_TAG='${barcode_tag}'
    #end if

    VALIDATION_STRINGENCY='${validation_stringency}'
    QUIET=true
    VERBOSITY=ERROR

  ]]></command>
  <inputs>

        <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."/>

   <expand macro="VS" />

  </inputs>

                                The maximum offset between two duplicte clusters in order to consider them optical
                                duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels)
                                unless using later versions of the Illumina pipeline that multiply pixel values by 10, in
                                which case 50-100 is more normal.  Default value: 100.

  BARCODE_TAG=String            Barcode SAM tag (ex. BC for 10X Genomics)  Default value: null.

@more_info@

  </help>
</tool>