comparison picard_CollectInsertSizeMetrics.xml @ 8:e417b1d6288d draft

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

7:08f69add4d06

  <expand macro="requirements">
    <requirement type="package" version="3.3.1">r</requirement>
  </expand>
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"
    
    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if
    
    picard
    CollectInsertSizeMetrics
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    HISTOGRAM_FILE="${histFile}"
    DEVIATIONS="${deviations}"
    
    #if str( $hist_width ):
      HISTOGRAM_WIDTH="${hist_width}"
    #end if
    
    MINIMUM_PCT="${min_pct}"
    REFERENCE_SEQUENCE="${reference_fasta_filename}"
    ASSUME_SORTED="${assume_sorted}"
    METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"

    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">

      <option value="ALL_READS" selected="True">All reads</option>
      <option value="SAMPLE">Sample</option>
      <option value="LIBRARY">Library</option>
      <option value="READ_GROUP">Read group</option>
    </param>
    
    <expand macro="VS" />
    
  </inputs>
  
  <outputs>
    <data format="tabular" name="outFile"/>
    <data format="pdf" name="histFile"/>
  </outputs>
  
  <tests>
    <test>
      <param name="metric_accumulation_level" value="ALL_READS"/>
      <param name="deviations" value="10.0" />
      <param name="hist_width" value="500" />

      <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
      <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
      <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>
  
  
  <help>

.. class:: infomark

**Purpose**

@dataset_collections@

@description@

 
  DEVIATIONS=Double             Generate mean, sd and plots by trimming the data down to MEDIAN + 
                                DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically 
                                includes enough anomalous values from chimeras and other artifacts to make the mean and 
                                sd grossly misleading regarding the real distribution.  Default value: 10.0. 

  HISTOGRAM_WIDTH=Integer
  W=Integer                     Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. 
                                Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be 
                                included.  Default value: not set. 

  MINIMUM_PCT=Float
  M=Float                       When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that 
                                have fewer than this percentage of overall reads. (Range: 0 to 1).  Default value: 0.05. 

  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. 
 
  ASSUME_SORTED=Boolean
  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default 
                                value: true. This option can be set to 'null' to clear the default value. Possible 
                                values: {true, false}
                                
@more_info@

  </help>
</tool>

8:e417b1d6288d

  <expand macro="requirements">
    <requirement type="package" version="3.3.1">r</requirement>
  </expand>
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    picard
    CollectInsertSizeMetrics
    INPUT='$inputFile.element_identifier'
    OUTPUT="${outFile}"
    HISTOGRAM_FILE="${histFile}"
    DEVIATIONS="${deviations}"

    #if str( $hist_width ):
      HISTOGRAM_WIDTH="${hist_width}"
    #end if

    MINIMUM_PCT="${min_pct}"
    REFERENCE_SEQUENCE="${reference_fasta_filename}"
    ASSUME_SORTED="${assume_sorted}"
    METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"

    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">

      <option value="ALL_READS" selected="True">All reads</option>
      <option value="SAMPLE">Sample</option>
      <option value="LIBRARY">Library</option>
      <option value="READ_GROUP">Read group</option>
    </param>

    <expand macro="VS" />

  </inputs>

  <outputs>
    <data format="tabular" name="outFile"/>
    <data format="pdf" name="histFile"/>
  </outputs>

  <tests>
    <test>
      <param name="metric_accumulation_level" value="ALL_READS"/>
      <param name="deviations" value="10.0" />
      <param name="hist_width" value="500" />

      <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" />
      <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" />
      <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/>
    </test>
  </tests>


  <help>

.. class:: infomark

**Purpose**

@dataset_collections@

@description@


  DEVIATIONS=Double             Generate mean, sd and plots by trimming the data down to MEDIAN +
                                DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically
                                includes enough anomalous values from chimeras and other artifacts to make the mean and
                                sd grossly misleading regarding the real distribution.  Default value: 10.0.

  HISTOGRAM_WIDTH=Integer
  W=Integer                     Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail.
                                Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be
                                included.  Default value: not set.

  MINIMUM_PCT=Float
  M=Float                       When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that
                                have fewer than this percentage of overall reads. (Range: 0 to 1).  Default value: 0.05.

  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.

  ASSUME_SORTED=Boolean
  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.  Default
                                value: true. This option can be set to 'null' to clear the default value. Possible
                                values: {true, false}

@more_info@

  </help>
</tool>