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comparison extract_transcript_to_gene_map_from_trinity.xml @ 1:1ff2fc8da328

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Updates to rsem_calculate_expression.xml
author Jim Johnson <jj@umn.edu>
date Thu, 05 Dec 2013 10:54:28 -0600
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children f6b8155ab12a
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0:64d45f959303 1:1ff2fc8da328
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 $map_file
8 </command>
9
10 <inputs>
11 <param name="trinity_fasta_file" type="data" format="fasta" label="Trinity fasta file" />
12 </inputs>
13 <stdio>
14 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
15 </stdio>
16 <outputs>
17 <data format="tabular" name="map_file" label="${sample} gene map file"/>
18 </outputs>
19 <help>
20
21
22 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
23
24 NAME
25 extract-transcript-to-gene-map-from-trinity
26
27 SYNOPSIS
28 extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
29
30 DESCRIPTION
31 generates a gene_mp_file from a trinity fasta file
32
33
34 </help>
35 </tool>