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view picard_MeanQualityByCylce.xml @ 121:67f1ec3ab183 draft
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author | devteam |
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date | Wed, 26 Feb 2014 00:24:03 -0500 |
parents | 21bf2afb895c |
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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>