comparison picard_CollectAlignmentSummaryMetrics.xml @ 8:e417b1d6288d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit bf94a1505c131fb3f67c867b6e1d886780efa42e

7:08f69add4d06

    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":

        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    picard
    CollectAlignmentSummaryMetrics
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    MAX_INSERT_SIZE=${maxinsert}
    #for $sequence in $adapters:
        ADAPTER_SEQUENCE="${sequence.adapter}"
    #end for

    ASSUME_SORTED="${assume_sorted}"

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  ]]></command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">

@dataset_collections@

@description@

  MAX_INSERT_SIZE=Integer       Paired end reads above this insert size will be considered chimeric along with 
                                inter-chromosomal pairs.  Default value: 100000.  

  ADAPTER_SEQUENCE=String       List of adapter sequences to use when processing the alignment metrics  This option may 
                                be specified 0 or more times.  

  METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
  LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE, 
                                LIBRARY, READ_GROUP} This option may be specified 0 or more times.  

  IS_BISULFITE_SEQUENCED=Boolean
  BS=Boolean                    Whether the SAM or BAM file consists of bisulfite sequenced reads.    


  REFERENCE_SEQUENCE=File
  R=File                        Reference sequence fasta  Default value: null. 

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true (default), then the sort order in the header file will be ignored. 

@more_info@

  </help>
</tool>

8:e417b1d6288d

    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":

        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    picard
    CollectAlignmentSummaryMetrics
    INPUT='$inputFile.element_identifier'
    OUTPUT="${outFile}"
    MAX_INSERT_SIZE=${maxinsert}
    #for $sequence in $adapters:
        ADAPTER_SEQUENCE="${sequence.adapter}"
    #end for

    ASSUME_SORTED="${assume_sorted}"

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

  ]]></command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">

@dataset_collections@

@description@

  MAX_INSERT_SIZE=Integer       Paired end reads above this insert size will be considered chimeric along with
                                inter-chromosomal pairs.  Default value: 100000.

  ADAPTER_SEQUENCE=String       List of adapter sequences to use when processing the alignment metrics  This option may
                                be specified 0 or more times.

  METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel
  LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics.    Possible values: {ALL_READS, SAMPLE,
                                LIBRARY, READ_GROUP} This option may be specified 0 or more times.

  IS_BISULFITE_SEQUENCED=Boolean
  BS=Boolean                    Whether the SAM or BAM file consists of bisulfite sequenced reads.


  REFERENCE_SEQUENCE=File
  R=File                        Reference sequence fasta  Default value: null.

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.

@more_info@

  </help>
</tool>