Mercurial > repos > iuc > trinity_gene_to_trans_map
comparison gene_to_trans_map.xml @ 0:1bbdff0c4dba draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
| author | iuc |
|---|---|
| date | Mon, 01 Aug 2016 11:51:48 -0400 |
| parents | |
| children | aad66a0cda96 |
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| -1:000000000000 | 0:1bbdff0c4dba |
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| 1 <tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@.0"> | |
| 2 <description>for Trinity assembly</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <expand macro="stdio"/> | |
| 8 <command><![CDATA[ | |
| 9 get_Trinity_gene_to_trans_map.pl "$assembly" > "$map" | |
| 10 ]]></command> | |
| 11 <inputs> | |
| 12 <param format="fasta" name="assembly" type="data" label="Trinity assembly"/> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="tabular" name="map" label="${tool.name} on ${on_string}: Genes to transcripts map"/> | |
| 16 </outputs> | |
| 17 <tests> | |
| 18 <test> | |
| 19 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> | |
| 20 <output name="map" file="raw/map.tsv" /> | |
| 21 </test> | |
| 22 </tests> | |
| 23 <help> | |
| 24 Trinity_ assembles transcript sequences from Illumina RNA-Seq data. | |
| 25 This tool produces a file containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity. | |
| 26 The output file is intended to be used by the "Align reads and estimate abundance" tool. | |
| 27 | |
| 28 .. _Trinity: http://trinityrnaseq.github.io | |
| 29 </help> | |
| 30 | |
| 31 <expand macro="citation" /> | |
| 32 </tool> |