comparison picard_MarkDuplicates.xml @ 27:fdca9493e09b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 70d2a66c405be58d4413753792bcadf212a4da84

26:fc3866ddc7b6

<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@">3</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

    </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. Typically 'RX' "/>

   <expand macro="VS" />

  </inputs>

  <outputs>
    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>
    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/>
  </outputs>

  <tests>
    <test>
      <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>

27:fdca9493e09b

<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@">4</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

    </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="5000" 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>

  <outputs>
    <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: tabular"/>
    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM"/>
  </outputs>

  <tests>
    <test>
      <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/>