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comparison picard_CollectRnaSeqMetrics.xml @ 11:3d8d70436d02 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Wed, 08 Feb 2017 12:41:25 -0500
parents 126c30841c38
children a459ead5ab75
comparison
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10:126c30841c38 11:3d8d70436d02
226 REF_FLAT=File Gene annotations in refFlat form. Format described here: 226 REF_FLAT=File Gene annotations in refFlat form. Format described here:
227 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required. 227 http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required.
228 228
229 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases 229 RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases
230 will be identified as being ribosomal. Format described here: 230 will be identified as being ribosomal. Format described here:
231 http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html and can be 231 https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/util/IntervalList.html and can be
232 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool 232 generated from BED datasetes using Galaxy's wrapper for picard_BedToIntervalList tool
233 233
234 STRAND_SPECIFICITY=StrandSpecificity 234 STRAND_SPECIFICITY=StrandSpecificity
235 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND 235 STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND
236 if the reads are expected to be on the transcription strand. Required. Possible values: 236 if the reads are expected to be on the transcription strand. Required. Possible values:
237 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND} 237 {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND}