comparison picard_MarkDuplicates.xml @ 25:7d34178f2812 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a0fcbda330469051d130fd0802c55960ae948e3b

24:b9fbec5ac6b2

<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

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

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

    VALIDATION_STRINGENCY='${validation_stringency}'

    <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."/>

   <expand macro="VS" />

  </inputs>

      <param name="remove_duplicates" value="False"/>
      <param name="read_name_regex" value=""/>
      <param name="optical_duplicate_pixel_distance" value="100"/>
      <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>

25:7d34178f2812

<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>examine aligned records in BAM datasets to locate duplicate molecules</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">2</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

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

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

    VALIDATION_STRINGENCY='${validation_stringency}'

    <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. Typically 'RX' "/>

   <expand macro="VS" />

  </inputs>

      <param name="remove_duplicates" value="False"/>
      <param name="read_name_regex" value=""/>
      <param name="optical_duplicate_pixel_distance" value="100"/>
      <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
      <param name="validation_stringency" value="LENIENT"/>
      <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
    </test>
    <test>
      <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>
      <param name="comment" value="test-run"/>
      <param name="assume_sorted" value="True"/>
      <param name="remove_duplicates" value="False"/>
      <param name="read_name_regex" value=""/>
      <param name="optical_duplicate_pixel_distance" value="100"/>
      <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/>
      <param name="validation_stringency" value="LENIENT"/>
      <param name='barcode_tag' value="RX"/>
      <output name="outFile" file="picard_MarkDuplicates_test2.bam" ftype="bam" lines_diff="4"/>
    </test>
  </tests>