view picard_MeanQualityByCycle.xml @ 135:1790970e47fe draft

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<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.106.0">
<description>Calculates mean quality by cycle</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}
    --pfreadsonly ${PF_READS_ONLY} --alignedreadsonly ${ALIGNED_READS_ONLY}
    -j "\$JAVA_JAR_PATH/MeanQualityByCycle.jar"
  </command>
   
  <stdio>
    <exit_code range="0" level="warning" description="Tool finished correctly" />
  </stdio>
   
  <inputs>
      <param format="sam,bam" name="input_file" type="data" label="Input SAM or BAM file. Required." help="" />
      <param checked="False" truevalue="true" falsevalue="false" name="ALIGNED_READS_ONLY" type="boolean" label="If set to true, calculate mean quality over aligned reads only." help="" />
      <param checked="False" truevalue="true" falsevalue="false" name="PF_READS_ONLY" type="boolean" label="If set to true calculate mean quality over PF reads only." help="" />
      <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." />
      <param name="out_prefix" value="Mean quality by cycle" type="text"
      label="Title for the output file" help="Use this remind you what the job was for." size="80" />
  </inputs>
  <outputs>
		<data format="html" name="html_file"  label="${out_prefix}.html"/>
  </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. // Actually, this does not seem to be used anywhere in the tool -- so we removed it
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>