Mercurial > repos > devteam > picard1106
diff picard_CollectRnaSeqMetrics.xml @ 129:03ed36a962af draft
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author | devteam |
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date | Wed, 26 Feb 2014 02:10:19 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectRnaSeqMetrics.xml Wed Feb 26 02:10:19 2014 -0500 @@ -0,0 +1,98 @@ +<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>