annotate picard_AddOrReplaceReadGroups.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>add or replaces read group information</description>
    <macros>
        <import>picard_macros.xml</import>
        <import>read_group_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
    @define_read_group_helpers@
    #set $rg_auto_name = $read_group_name_default($inputFile)
    @set_read_group_vars@
    @java_options@
    @symlink_element_identifier@
    picard AddOrReplaceReadGroups
      --INPUT '$escaped_element_identifier'
      $format_read_group("", $rg_lb, quote='"', arg=" --RGLB ")
      $format_read_group("", $rg_pl, quote='"', arg=" --RGPL ")
      $format_read_group("", $rg_pu, quote='"', arg=" --RGPU ")
      $format_read_group("", $rg_sm, quote='"', arg=" --RGSM ")
      $format_read_group("", $rg_id, quote='"', arg=" --RGID ")
      $format_read_group("", $rg_ds, quote='"', arg=" --RGDS ")
      $format_read_group("", $rg_pi, quote='"', arg=" --RGPI ")
      $format_read_group("", $rg_dt, quote='"', arg=" --RGDT ")
      --OUTPUT '${outFile}'
      --VALIDATION_STRINGENCY '${validation_stringency}'
      --QUIET true
      --VERBOSITY ERROR

  ]]></command>
    <inputs>
        <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
        <expand macro="read_group_inputs_picard"/>
        <expand macro="VS"/>
    </inputs>
    <outputs>
        <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with replaced/modified readgroups"/>
    </outputs>
    <tests>
        <test>
            <param name="inputFile" value="picard_ARRG.bam"/>
            <param name="LB" value="tumor-a"/>
            <param name="PL" value="ILLUMINA"/>
            <param name="PU" value="run-1"/>
            <param name="SM" value="sample-a"/>
            <param name="ID" value="id-1"/>
            <output name="outFile" file="picard_ARRG_test1.bam" ftype="bam"/>
        </test>
    </tests>
    <help>

.. class:: infomark

**Purpose**

Add or Replace Read Groups in an input BAM or SAM file.

@dataset_collections@

@RG@

@description@

  INPUT=File
  I=File                  Input file (bam or sam).  Required.

  OUTPUT=File
  O=File                  Output file (bam or sam).  Required.

  SORT_ORDER=SortOrder
  SO=SortOrder            Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT.
                          Default value: null. Possible values: {unsorted, queryname, coordinate}

  RGID=String
  ID=String               Read Group ID  Default value: 1. This option can be set to 'null' to clear the default
                          value.

  RGLB=String
  LB=String               Read Group Library  Required.

  RGPL=String
  PL=String               Read Group platform (e.g. illumina, solid)  Required.

  RGPU=String
  PU=String               Read Group platform unit (eg. run barcode)  Required.

  RGSM=String
  SM=String               Read Group sample name  Required.

  RGCN=String
  CN=String               Read Group sequencing center name  Default value: null.

  RGDS=String
  DS=String               Read Group description  Default value: null.

  RGDT=Iso8601Date
  DT=Iso8601Date          Read Group run date  Default value: null.

  RGPI=Integer
  PI=Integer              Read Group predicted insert size  Default value: null.

@more_info@
  </help>
    <expand macro="citations"/>
</tool>