view picard_CollectRnaSeqMetrics.xml @ 129:03ed36a962af draft

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<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.106.0">
<description>Collect RNA-Seq Metrics</description>
<requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
   <command interpreter="python">
      picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"
    -n "${out_prefix}" --tmpdir "${__new_file_path__}" --assumesorted ${ASSUME_SORTED}
    --refflat ${REF_FLAT}
    #if $identify_ribosomal.opt == "yes"
    	--ribosomalintervals ${identify_ribosomal.RIBOSOMAL_INTERVALS}
    #end if
    --malevel "${malevel}"
    --minlength ${MINIMUM_LENGTH}
    --strandspecificity ${STRAND_SPECIFICITY}
    --rrnafragmentpercentage ${RRNA_FRAGMENT_PERCENTAGE}
    #for $i in $IGNORE_SEQUENCES
        --ignoreseq "${i.IGNORE_SEQUENCE}"
    #end for 
    -j "\$JAVA_JAR_PATH/CollectRnaSeqMetrics.jar"
  </command>
    
  <stdio>
    <exit_code range="0" level="warning" description="Tool finished correctly" />
  </stdio>
   
  <inputs>
  	<param format="sam" name="input_file" type="data" label="Input SAM file." help="" />
  
      <param format="data" name="REF_FLAT" type="data" label="Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required." help="" />
      
    <conditional name="identify_ribosomal">
      <param name="opt" type="select" label="Identify ribosomal bases" help="If 'no' is selected, no bases will be identified as being ribosomal.">
        <option value="no">no</option>
        <option value="yes">yes</option>
      </param>
      <when value="no" />
      <when value="yes">
        <param format="data" name="RIBOSOMAL_INTERVALS" type="data" label="Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described here: http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html Default value: null." help="" />
       </when>
    </conditional>      
      
      <param name="STRAND_SPECIFICITY" type="select" label="For strand-specific library prep." help="For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand. {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}">
            <option value="NONE" selected="True">None</option>
            <option value="FIRST_READ_TRANSCRIPTION_STRAND">FIRST_READ_TRANSCRIPTION_STRAND</option>
            <option value="SECOND_READ_TRANSCRIPTION_STRAND">SECOND_READ_TRANSCRIPTION_STRAND</option>
      </param>
      
      <param name="MINIMUM_LENGTH" type="text" value="500" label="When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater." help="" />
      
     <repeat name="IGNORE_SEQUENCES" title="Ignore Sequences">
      <param name="IGNORE_SEQUENCE" label="Ignore Sequence" type="text" help="If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases." />
    </repeat>
      
      <param name="RRNA_FRAGMENT_PERCENTAGE" type="text" value="0.8" label="This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair by this must in order to be considered rRNA." help="" />
      
      <param name="malevel" value="0" type="select" multiple="true"  label="Metric Accumulation Level"
      help="Level(s) at which metrics will be accumulated">
      <option value="ALL_READS" selected="true">All reads (default)</option>
      <option value="SAMPLE" default="true">Sample</option>
      <option value="LIBRARY" default="true">Library</option>
      <option value="READ_GROUP" default="true">Read group</option>
     </param>      
      
      <param  checked="True" truevalue="true" falsevalue="false" name="ASSUME_SORTED" type="boolean" label="If true (default), then the sort order in the header file will be ignored." />
  </inputs>
  <outputs>
    		<data format="html" name="html_file"  label="${out_prefix}.html"/>
  </outputs>
  <tests>
  <test>
    
    </test>
  </tests>
  <help>
Picard documentation says:
 
  
CollectRnaSeqMetrics

Documentation: http://picard.sourceforge.net/command-line-overview.shtml#CollectRnaSeqMetrics
Program to collect metrics about the alignment of RNA to various functional classes of loci in the genome: coding, intronic, UTR, intergenic, ribosomal. Also determines strand-specificity for strand-specific libraries.
Option	Description
REF_FLAT=File	Gene annotations in refFlat form. Format described here: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required.
RIBOSOMAL_INTERVALS=File	Location of rRNA sequences in genome, in interval_list format. If not specified no bases will be identified as being ribosomal. Format described here: http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html Default value: null.
STRAND_SPECIFICITY=StrandSpecificity	For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand. Required. Possible values: {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}
MINIMUM_LENGTH=Integer	When calculating coverage based values (e.g. CV of coverage) only use transcripts of this length or greater. Default value: 500. This option can be set to 'null' to clear the default value.
CHART_OUTPUT=File	The PDF file to write out a plot of normalized position vs. coverage. Default value: null.
IGNORE_SEQUENCE=String	If a read maps to a sequence specified with this option, all the bases in the read are counted as ignored bases. These reads are not counted as This option may be specified 0 or more times.
RRNA_FRAGMENT_PERCENTAGE=Double	This percentage of the length of a fragment must overlap one of the ribosomal intervals for a read or read pair by this must in order to be considered rRNA. Default value: 0.8. This option can be set to 'null' to clear the default value.
METRIC_ACCUMULATION_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. This option can be set to 'null' to clear the default list.
INPUT=File	Input SAM or BAM file. Required.
OUTPUT=File	File to write the output to. Required.
REFERENCE_SEQUENCE=File	Reference sequence fasta Default value: null.
ASSUME_SORTED=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}
STOP_AFTER=Long	Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value. 

 
  </help>
</tool>