Mercurial > repos > devteam > picard
comparison picard_CollectRnaSeqMetrics.xml @ 12:a459ead5ab75 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit a55cff7dfc145ed17ec2ee9f6a70d51c6f9d74b6
author | iuc |
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date | Thu, 13 Apr 2017 19:09:04 -0400 |
parents | 3d8d70436d02 |
children | 486d7500da69 |
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11:3d8d70436d02 | 12:a459ead5ab75 |
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217 7. Click **done with selection** | 217 7. Click **done with selection** |
218 8. Click **Send query to Galaxy** | 218 8. Click **Send query to Galaxy** |
219 9. A new dataset will appear in the current Galaxy history | 219 9. A new dataset will appear in the current Galaxy history |
220 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool | 220 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool |
221 | 221 |
222 .. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat | 222 .. _refFlat: https://genome.ucsc.edu/FAQ/FAQformat.html#format9 |
223 | 223 |
224 @description@ | 224 @description@ |
225 | 225 |
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 https://genome.ucsc.edu/FAQ/FAQformat.html#format9 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 https://samtools.github.io/htsjdk/javadoc/htsjdk/htsjdk/samtools/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 |