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comparison extract_transcript_to_gene_map_from_trinity.xml @ 0:ca988deacfd1

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author jjohnson
date Fri, 07 Feb 2014 08:07:29 -0500
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1 <tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="1.1.17">
2 <description>extract transcript to gene map from trinity</description>
3 <requirements>
4 <requirement type="package" version="1.1.17">rsem</requirement>
5 </requirements>
6 <command>
7 extract-transcript-to-gene-map-from-trinity $trinity_fasta_file $map_file
8 </command>
9
10 <inputs>
11 <param name="trinity_fasta_file" type="data" format="fasta" label="Trinity fasta file" />
12 </inputs>
13 <stdio>
14 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
15 </stdio>
16 <outputs>
17 <data format="tabular" name="map_file" label="${tool.name} on ${on_string}: gene map file"/>
18 </outputs>
19 <tests>
20 <test>
21 <param name="trinity_fasta_file" value="trinity_assembled_transcripts.fasta" ftype="fasta"/>
22 <output name="map_file" file="trinity_gene_map.tabular"/>
23 </test>
24 </tests>
25 <help>
26
27
28 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
29
30 NAME
31 extract-transcript-to-gene-map-from-trinity
32
33 SYNOPSIS
34 extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
35
36 DESCRIPTION
37 generates a gene_mp_file from a trinity fasta file
38
39
40 </help>
41 </tool>