Mercurial > repos > iuc > trinity_super_transcripts

comparison super_transcripts.xml @ 3:b34de8dc0f64 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"
author iuc
date Fri, 01 Nov 2019 08:10:22 -0400
parents 64094e19077d
children 18a069ea4b96
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2:3abd51c4b151 3:b34de8dc0f64
16 <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/> 16 <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/>
17 </outputs> 17 </outputs>
18 <tests> 18 <tests>
19 <test> 19 <test>
20 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> 20 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
21 <output name="seqs" file="supertranscripts/trinity_genes.fasta" /> 21 <output name="seqs" file="supertranscripts/trinity_genes.fasta" sort="True" />
22 <output name="annotation" file="supertranscripts/trinity_genes.gtf" /> 22 <output name="annotation" file="supertranscripts/trinity_genes.gtf" sort="True" />
23 <output name="malign" file="supertranscripts/trinity_genes.malign" /> 23 <output name="malign" file="supertranscripts/trinity_genes.malign" />
24 </test> 24 </test>
25 </tests> 25 </tests>
26 <help> 26 <help>
27 SuperTranscripts provide a gene-like view of the transcriptional complexity of a gene. SuperTranscripts were originally defined by Nadia Davidson, Anthony Hawkins, and Alicia Oshlack as described in their publication "SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes" Genome Biology, 2017. SuperTranscripts are useful in the context of genome-free de novo transcriptome assembly in that they provide a genome-like reference for studying aspects of the gene including differential transcript usage (aka. differential exon usage) and as a substrate for mapping reads and identifying allelic polymorphisms. 27 SuperTranscripts provide a gene-like view of the transcriptional complexity of a gene. SuperTranscripts were originally defined by Nadia Davidson, Anthony Hawkins, and Alicia Oshlack as described in their publication "SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes" Genome Biology, 2017. SuperTranscripts are useful in the context of genome-free de novo transcriptome assembly in that they provide a genome-like reference for studying aspects of the gene including differential transcript usage (aka. differential exon usage) and as a substrate for mapping reads and identifying allelic polymorphisms.