Mercurial > repos > artbio > rsem
comparison extract_transcript_to_gene_map_from_trinity.xml @ 0:e5e836936d60 draft
planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80
| author | artbio |
|---|---|
| date | Sat, 31 Mar 2018 21:30:07 -0400 |
| parents | |
| children | 49795544dac7 |
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| -1:000000000000 | 0:e5e836936d60 |
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| 1 <tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="0.4.0"> | |
| 2 <description>extract transcript to gene map from trinity</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.3.0">rsem</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> | |
| 8 </stdio> | |
| 9 <command> | |
| 10 extract-transcript-to-gene-map-from-trinity $trinity_fasta_file $map_file | |
| 11 </command> | |
| 12 <inputs> | |
| 13 <param name="trinity_fasta_file" type="data" format="fasta" label="Trinity fasta file" /> | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data format="tabular" name="map_file" label="${tool.name} on ${on_string}: gene map file"/> | |
| 17 </outputs> | |
| 18 <tests> | |
| 19 <test> | |
| 20 <param name="trinity_fasta_file" value="trinity_assembled_transcripts.fasta" ftype="fasta"/> | |
| 21 <output name="map_file" file="trinity_gene_map.tabular"/> | |
| 22 </test> | |
| 23 </tests> | |
| 24 <help> | |
| 25 | |
| 26 | |
| 27 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ | |
| 28 | |
| 29 NAME | |
| 30 extract-transcript-to-gene-map-from-trinity | |
| 31 | |
| 32 SYNOPSIS | |
| 33 extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file | |
| 34 | |
| 35 DESCRIPTION | |
| 36 generates a gene_mp_file from a trinity fasta file | |
| 37 | |
| 38 | |
| 39 </help> | |
| 40 <citations> | |
| 41 <citation type="doi">10.1038/nbt.1883</citation> | |
| 42 </citations> | |
| 43 </tool> |