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comparison cpo_clustalw.xml @ 1:fea89c4d5227 draft

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author jjjjia
date Thu, 16 Aug 2018 19:27:05 -0400
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0:917a05a03ac9 1:fea89c4d5227
1 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
2 <description>makes tree from alignment</description>
3 <requirements>
4 <requirement type="package" version="2.1">clustalw</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 clustalw2 -tree -infile=$input -outputtree=nj
9 ]]>
10 </command>
11 <inputs>
12 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
13 </inputs>
14 <outputs>
15 <data name="phylip" format="txt" from_work_dir="*.ph"/>
16 <data name="njtree" format="txt" from_work_dir="*.nj*"/>
17 </outputs>
18 <tests>
19 <test>
20 <param name="input" value="plasmid_476.fasta" ftype="fasta"/>
21 <section name="adv_param">
22 <param name="evalue" value="0.00001"/>
23 <param name="unicycler_contigs" value="True"/>
24 <param name="run_circlator" value="True"/>
25 </section>
26 <output name="outfile1">
27 <assert_contents>
28 <has_text text="NC_019097"/>
29 </assert_contents>
30 </output>
31 </test>
32 </tests>
33 <help>
34
35 **Syntax**
36
37 This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
38
39 For more information please visit https://github.com/phac-nml/mob-suite/.
40
41 -----
42
43 **Input:**
44
45 A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
46
47
48 **Output:**
49
50 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.
51
52 Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.
53
54
55 </help>
56 <citations>
57 <citation type="bibtex">
58 @misc{githubmob-suite,
59 author = {Robertson J, Nash J},
60 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
61 publisher = {GitHub},
62 journal = {GitHub repository},
63 doi = {10.1099/mgen.0.000206},
64 url = {https://github.com/phac-nml/mob-suite}
65 }</citation>
66 </citations>
67 </tool>