comparison picard_CollectRnaSeqMetrics.xml @ 16:6741a8ace658 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1

15:00fe2ff64467

   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  and can be
				 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool

   STRAND_SPECIFICITY=StrandSpecificity
   STRAND=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}

16:6741a8ace658

   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:
                                 https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html and can be
                                 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool

   STRAND_SPECIFICITY=StrandSpecificity
   STRAND=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}