Mercurial > repos > iuc > trinity_super_transcripts
comparison super_transcripts.xml @ 0:64094e19077d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
| author | iuc |
|---|---|
| date | Thu, 14 Jun 2018 03:12:34 -0400 |
| parents | |
| children | b34de8dc0f64 |
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| -1:000000000000 | 0:64094e19077d |
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| 1 <tool id="trinity_super_transcripts" name="Generate SuperTranscripts" version="@WRAPPER_VERSION@"> | |
| 2 <description>from a Trinity assembly</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <command detect_errors="aggressive"><![CDATA[ | |
| 8 Trinity_gene_splice_modeler.py --incl_malign --trinity_fasta '$assembly' | |
| 9 ]]></command> | |
| 10 <inputs> | |
| 11 <param format="fasta" name="assembly" type="data" label="Trinity assembly"/> | |
| 12 </inputs> | |
| 13 <outputs> | |
| 14 <data format="fasta" name="seqs" from_work_dir="trinity_genes.fasta" label="${tool.name} on ${on_string}: SuperTranscripts sequences"/> | |
| 15 <data format="gtf" name="annotation" from_work_dir="trinity_genes.gtf" label="${tool.name} on ${on_string}: SuperTranscripts strcture annotation"/> | |
| 16 <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> | |
| 21 <output name="seqs" file="supertranscripts/trinity_genes.fasta" /> | |
| 22 <output name="annotation" file="supertranscripts/trinity_genes.gtf" /> | |
| 23 <output name="malign" file="supertranscripts/trinity_genes.malign" /> | |
| 24 </test> | |
| 25 </tests> | |
| 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. | |
| 28 | |
| 29 A SuperTranscript is constructed by collapsing unique and common sequence regions among splicing isoforms into a single linear sequence. | |
| 30 | |
| 31 .. _Trinity: http://trinityrnaseq.github.io | |
| 32 </help> | |
| 33 | |
| 34 <expand macro="citation" /> | |
| 35 </tool> |