Mercurial > repos > jjohnson > arriba
comparison arriba_get_filters.xml @ 4:77021ad5037d draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
author | jjohnson |
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date | Sat, 09 Oct 2021 15:41:49 +0000 |
parents | 7420753b0671 |
children | 005b200c8841 |
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3:2d32e6c86c48 | 4:77021ad5037d |
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32 <option value="GRCm38">GRCm38</option> | 32 <option value="GRCm38">GRCm38</option> |
33 <option value="mm10">mm10</option> | 33 <option value="mm10">mm10</option> |
34 </param> | 34 </param> |
35 </inputs> | 35 </inputs> |
36 <outputs> | 36 <outputs> |
37 <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist"/> | 37 <data name="blacklist" format="tabular" label="${tool.name} ${arriba_reference_name} blacklist.tsv"/> |
38 <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions"/> | 38 <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions.tsv"/> |
39 <data name="protein_domains" format="tabular" label="${tool.name} ${arriba_reference_name} protein_domains"/> | 39 <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> |
40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands"/> | 40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> |
41 </outputs> | 41 </outputs> |
42 <tests> | |
43 <test> | |
44 <param name="arriba_reference_name" value="GRCh38"/> | |
45 <output name="cytobands"> | |
46 <assert_contents> | |
47 <has_text_matching expression="1\t1\t\d+\tp36.33\tgneg"/> | |
48 </assert_contents> | |
49 </output> | |
50 </test> | |
51 </tests> | |
42 <help><![CDATA[ | 52 <help><![CDATA[ |
43 ** Arriba ** | 53 ** Arriba ** |
44 | 54 |
45 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. | 55 Arriba_ is a fast tool to search for aberrant transcripts such as gene fusions. |
46 It is based on chimeric alignments found by the STAR RNA-Seq aligner. | 56 It is based on chimeric alignments found by the STAR RNA-Seq aligner. |