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comparison cpo_clustalw.xml @ 6:cabceaa239e4 draft

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author jjjjia
date Thu, 23 Aug 2018 12:21:15 -0400
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5:698579246d0d 6:cabceaa239e4
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1">clustalw</requirement> 4 <requirement type="package" version="2.1">clustalw</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"> 6 <command detect_errors="exit_code">
7 <![CDATA[ 7 <![CDATA[
8 clustalw2 -tree -infile=$input -outputtree=nj 8 clustalw2 -tree -infile=$input && mv `ls $input | cut -d$'.' -f 1`.ph ./result.ph
9 ]]> 9 ]]>
10 </command> 10 </command>
11 <inputs> 11 <inputs>
12 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/> 12 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
13 </inputs> 13 </inputs>
14 <outputs> 14 <outputs>
15 <data name="phylip" format="txt" from_work_dir="*.ph"/> 15 <data name="phylip" format="txt" from_work_dir="result.ph"/>
16 <data name="njtree" format="txt" from_work_dir="*.nj*"/>
17 </outputs> 16 </outputs>
18 <help> 17 <help>
19 18 clustalw2 -tree -infile=$input -outputtree=nj
20 **Syntax**
21
22 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
23
24 For more information please visit https://github.com/phac-nml/mob-suite/.
25
26 -----
27
28 **Input:**
29
30 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
31
32
33 **Output:**
34
35 Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
36
37 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
38
39
40 </help> 19 </help>
41 <citations> 20 <citations>
42 <citation type="bibtex"> 21 <citation type="bibtex">
43 @misc{githubmob-suite, 22 @misc{githubmob-suite,
44 author = {Robertson J, Nash J}, 23 author = {Robertson J, Nash J},