Mercurial > repos > jjohnson > arriba
comparison arriba_get_filters.xml @ 5:005b200c8841 draft
"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit bdefea23247f7d999b96e232ce810e2887338680"
author | jjohnson |
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date | Sun, 10 Oct 2021 13:00:45 +0000 |
parents | 77021ad5037d |
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4:77021ad5037d | 5:005b200c8841 |
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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} ${arriba_reference_name} blacklist.tsv"/> | 37 <data name="blacklist" format="tabular.gz" label="${tool.name} ${arriba_reference_name} blacklist.tsv.gz"/> |
38 <data name="known_fusions" format="tabular" label="${tool.name} ${arriba_reference_name} known_fusions.tsv"/> | 38 <data name="known_fusions" format="tabular.gz" label="${tool.name} ${arriba_reference_name} known_fusions.tsv.gz"/> |
39 <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> | 39 <data name="protein_domains" format="gff3" label="${tool.name} ${arriba_reference_name} protein_domains.gff3"/> |
40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> | 40 <data name="cytobands" format="tabular" label="${tool.name} ${arriba_reference_name} cytobands.tsv"/> |
41 </outputs> | 41 </outputs> |
42 <tests> | 42 <tests> |
43 <test> | 43 <test> |
48 </assert_contents> | 48 </assert_contents> |
49 </output> | 49 </output> |
50 </test> | 50 </test> |
51 </tests> | 51 </tests> |
52 <help><![CDATA[ | 52 <help><![CDATA[ |
53 ** Arriba ** | 53 **Arriba Get Filters** |
54 | 54 |
55 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. |
56 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. |
57 | 57 |
58 The **Arriba Get Filters** tool adds the following Arriba distribution input_files_ to your galaxy history: | |
59 | |
60 - blacklist | |
61 - known_fusions | |
62 - protein_domains | |
63 - cytobands | |
64 | |
65 | |
58 .. _Arriba: https://arriba.readthedocs.io/en/latest/ | 66 .. _Arriba: https://arriba.readthedocs.io/en/latest/ |
67 .. _input_files: https://arriba.readthedocs.io/en/latest/input-files/ | |
59 | 68 |
60 ]]></help> | 69 ]]></help> |
61 <expand macro="citations" /> | 70 <expand macro="citations" /> |
62 </tool> | 71 </tool> |