Mercurial > repos > iuc > trinity_super_transcripts

annotate super_transcripts.xml @ 10:3064aa8755a0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
author iuc
date Tue, 11 Apr 2023 19:53:33 +0000
parents 9c545f1c1a4e
children 5c1fc038df6b
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1 <tool id="trinity_super_transcripts" name="Generate SuperTranscripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>from a Trinity assembly</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 Trinity_gene_splice_modeler.py --incl_malign --trinity_fasta '$assembly'
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10 ]]></command>
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11 <inputs>
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12 <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
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13 </inputs>
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14 <outputs>
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15 <data format="fasta" name="seqs" from_work_dir="trinity_genes.fasta" label="${tool.name} on ${on_string}: SuperTranscripts sequences"/>
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16 <data format="gtf" name="annotation" from_work_dir="trinity_genes.gtf" label="${tool.name} on ${on_string}: SuperTranscripts strcture annotation"/>
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17 <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/>
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18 </outputs>
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19 <tests>
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20 <test>
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21 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
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22 <output name="seqs" file="supertranscripts/trinity_genes.fasta" sort="True" />
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23 <output name="annotation" file="supertranscripts/trinity_genes.gtf" sort="True" />
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24 <output name="malign" file="supertranscripts/trinity_genes.malign" />
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25 </test>
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26 </tests>
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27 <help>
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28 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.
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30 A SuperTranscript is constructed by collapsing unique and common sequence regions among splicing isoforms into a single linear sequence.
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32 .. _Trinity: http://trinityrnaseq.github.io
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33 </help>
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35 <expand macro="citation" />
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36 </tool>