Mercurial > repos > trinity_ctat > ctat_trinity_rnaseq

comparison ctat_trinity_rnaseq.xml @ 3:777b35c8ee3e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Trying newer trinity
author trinity_ctat
date Mon, 25 Jun 2018 16:38:28 -0400
parents 8291ea96690f
children
comparison
equal deleted inserted replaced
2:8291ea96690f 3:777b35c8ee3e
2 2
3 <!-- Original tool written by Jeremy Goecks, 3 <!-- Original tool written by Jeremy Goecks,
4 later development/maintenance by (in chronological order) 4 later development/maintenance by (in chronological order)
5 Brian Haas, Ben Fulton, Cicada Dennis 5 Brian Haas, Ben Fulton, Cicada Dennis
6 --> 6 -->
7 <description>De novo assembly of RNA-Seq data using Trinity 2.4.0</description> 7 <description>De novo assembly of RNA-Seq data using Trinity</description>
8 <requirements> 8 <requirements>
9 <requirement type="package" version="2.7">python</requirement> 9 <requirement type="package" version="2.7">python</requirement>
10 <requirement type="package">subprocess32</requirement> 10 <requirement type="package">subprocess32</requirement>
11 <requirement type="package">samtools</requirement>
12 <requirement type="package">bzip2</requirement> 11 <requirement type="package">bzip2</requirement>
13 <requirement type="package" version="1.3.0">rsem</requirement> 12 <requirement type="package" version="1.3.0">rsem</requirement>
14 <requirement type="package" version="3">bioconductor-edger</requirement> 13 <requirement type="package" version="3">bioconductor-edger</requirement>
15 <requirement type="package" version="2">bioconductor-qvalue</requirement> 14 <requirement type="package" version="2">bioconductor-qvalue</requirement>
16 <requirement type="package" version="2.5.1">trinity</requirement> 15 <requirement type="package" version="2.6.6">trinity</requirement>
17 </requirements> 16 </requirements>
18 <command detect_errors="default"> 17 <command detect_errors="default">
19 <![CDATA[ 18 <![CDATA[
20 python $__tool_directory__/ctat_trinity_wrapper.py 19 python $__tool_directory__/ctat_trinity_wrapper.py
21 --CPU \${GALAXY_SLOTS:-4} 20 --CPU \${GALAXY_SLOTS:-4}
132 </assert_contents> 131 </assert_contents>
133 </output> 132 </output>
134 </test> 133 </test>
135 </tests> 134 </tests>
136 <help> 135 <help>
137 This instance is running Trinity version 2.4.0 and uses the following command: 136 This instance runs Trinity with the following command:
138 137
139 Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file 138 Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file
140 139
141 Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively. 140 Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively.
142 141