Mercurial > repos > jjohnson > arriba

comparison arriba_get_filters.xml @ 4:77021ad5037d draft

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"planemo upload for repository https://github.com/jj-umn/tools-iuc/tree/arriba/tools/arriba commit 5a62e8a2ec56a8ce00f89c8fbe61b3f1dffbbffd"
author jjohnson
date Sat, 09 Oct 2021 15:41:49 +0000
parents 7420753b0671
children 005b200c8841
comparison
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3:2d32e6c86c48 4:77021ad5037d
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.