view picard_MeanQualityByCylce.xml @ 118:21bf2afb895c draft

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<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.106.0">
<description>Calculates mean quality</description>
<requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
  <command interpreter="bash">
  	<!--	generic_outformat_wrapper.sh MeanQualityByCycle $outFile $outputFormat
 			CHART_OUTPUT=File	A file (with .pdf extension) to write the chart to. Required. 
 
          #if str( $ALIGNED_READS_ONLY ):
              ALIGNED_READS_ONLY="${ALIGNED_READS_ONLY}"
          #end if
          #if str( $PF_READS_ONLY ):
              PF_READS_ONLY="${PF_READS_ONLY}"
          #end if
          #if str( $INPUT ):
              INPUT="${INPUT}"
          #end if
          #if str( $OUTPUT ):
              OUTPUT="${OUTPUT}"
          #end if
          #if str( $REFERENCE_SEQUENCE ):
              REFERENCE_SEQUENCE="${REFERENCE_SEQUENCE}"
          #end if
          #if str( $ASSUME_SORTED ):
              ASSUME_SORTED="${ASSUME_SORTED}"
          #end if
          #if str( $STOP_AFTER ):
              STOP_AFTER="${STOP_AFTER}"
          #end if
 
      VALIDATION_STRINGENCY=LENIENT
      QUIET=True
      TMP_DIR="${__new_file_path__}" -->
  </command>
   
  <stdio>
    <exit_code range="0" level="warning" description="Tool finished correctly" />
  </stdio>
   
  <inputs>
   <!--
      <param format="XXCHANGEMEEE" name="ALIGNED_READS_ONLY" type="boolean" label="If set to true, calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
      <param format="XXCHANGEMEEE" name="PF_READS_ONLY" type="boolean" label="If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}" help="" />
      <param format="XXCHANGEMEEE" name="INPUT" type="data" label="Input SAM or BAM file. Required." help="" />
      <param format="XXCHANGEMEEE" name="OUTPUT" type="data" label="File to write the output to. Required." help="" />
      <param format="XXCHANGEMEEE" name="REFERENCE_SEQUENCE" type="data" label="Reference sequence fasta Default value: null." help="" />
      <param format="XXCHANGEMEEE" name="ASSUME_SORTED" type="boolean" label="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}" help="" />
      <param format="XXCHANGEMEEE" name="STOP_AFTER" type="string" label="Stop after processing N reads, mainly for debugging. Default value: 0. This option can be set to 'null' to clear the default value." help="" />
  -->
  </inputs>
  <outputs>
  <!--
    <data name="outFile" format="XXCHANGEMEEE">
  
    </data>
      -->
  </outputs>
  <tests>
  <test>
     <!-- Here is a command line that works:
        java -jar ...
     -->
     <!--
      <param name="inputFile" value="XXCHANGEMEE-input" />
      <output name="outFile" file="XXCHANGEMEE-correct-output" lines_diff="2" ftype="XXCHANGEMEE" />
        -->
    </test>
  </tests>
  <help>
Picard documentation says:
 
  
MeanQualityByCycle

Usage: program [options...]

Option	Description
CHART_OUTPUT=File	A file (with .pdf extension) to write the chart to. Required.
ALIGNED_READS_ONLY=Boolean	If set to true, calculate mean quality over aligned reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
PF_READS_ONLY=Boolean	If set to true calculate mean quality over PF reads only. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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>