Mercurial > repos > jjohnson > defuse
comparison defuse_trinity_analysis.xml @ 17:c3167ccca38c draft default tip
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit d2317dff5a89016f18038b97d057f47d949e7808-dirty
| author | jjohnson |
|---|---|
| date | Sat, 26 Jan 2019 12:53:08 -0500 |
| parents | bdd93719cede |
| children |
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| 16:bdd93719cede | 17:c3167ccca38c |
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| 38 <filter>(outputs and 'aligned' in outputs)</filter> | 38 <filter>(outputs and 'aligned' in outputs)</filter> |
| 39 </data> | 39 </data> |
| 40 <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/> | 40 <data name="output" metadata_source="defuse_results" format="tabular" label="${tool.name} on ${on_string}: Fusion Report"/> |
| 41 </outputs> | 41 </outputs> |
| 42 <tests> | 42 <tests> |
| 43 <test> | |
| 44 <param name="defuse_results" value="mm10_results.filtered.tsv" ftype="defuse.results.tsv" dbkey="mm10"/> | |
| 45 <output name="vcf" file="mm10_results.filtered.vcf"/> | |
| 46 </test> | |
| 47 </tests> | 43 </tests> |
| 48 <help> | 44 <help> |
| 49 **Defuse Results** | 45 **Defuse Results** |
| 50 | 46 |
| 51 Verifies DeFuse_ fusion predictions in results.tsv with TrinityRNAseq_ assembled transcripts and ORFs. | 47 Verifies DeFuse_ fusion predictions in results.tsv with TrinityRNAseq_ assembled transcripts and ORFs. |
| 52 | 48 |
| 53 This program relies on the header line of the results.tsv to determine which columns to use for analysis. | 49 DeFuse provides a total fusion sequence of 200-500 nucleotides (nts) around the fusion breakpoint. This may be insufficient to predict the effect of the fusion on protein production. To get a view of the full transcript containing the fusion, Trinity de novo transcripts from the RNA-seq data are compared with the deFuse fusion sequences using a subsequence around the deFuse indetified fusion breakpoint. The Trinity transcriptToOrfs output provides potential proteins from the projected fusion transcript. |
| 50 | |
| 51 This program relies on the header line of the deFuse results.tsv to determine which columns to use for analysis. | |
| 54 | 52 |
| 55 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse | 53 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse |
| 56 .. _TrinityRNAseq: http://trinityrnaseq.github.io/ | 54 .. _TrinityRNAseq: http://trinityrnaseq.github.io/ |
| 57 </help> | 55 </help> |
| 56 <expand macro="citations"> | |
| 57 <citation type="doi">10.1038/nbt.1883</citation> | |
| 58 <citation type="doi">10.1038/s41598-018-36840-z</citation> | |
| 59 </expand> | |
| 58 </tool> | 60 </tool> |