annotate cpo_clustalw.xml @ 6:cabceaa239e4 draft

planemo upload
author jjjjia
date Thu, 23 Aug 2018 12:21:15 -0400
parents 698579246d0d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
1 <tool id="cpo_clustalw" name="cpo_clustalw" version="2.1">
5
698579246d0d planemo upload
jjjjia
parents: 1
diff changeset
2 <description>Modified version of clustalw2 v2.1 to produce NJ trees from an SNIPPY produced alignment</description>
1
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
3 <requirements>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
4 <requirement type="package" version="2.1">clustalw</requirement>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
5 </requirements>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
6 <command detect_errors="exit_code">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
7 <![CDATA[
6
cabceaa239e4 planemo upload
jjjjia
parents: 5
diff changeset
8 clustalw2 -tree -infile=$input && mv `ls $input | cut -d$'.' -f 1`.ph ./result.ph
1
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
9 ]]>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
10 </command>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
11 <inputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
12 <param name="input" type="data" format="fasta" label="Input" help="FASTA file with contig(s)"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
13 </inputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
14 <outputs>
6
cabceaa239e4 planemo upload
jjjjia
parents: 5
diff changeset
15 <data name="phylip" format="txt" from_work_dir="result.ph"/>
1
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
16 </outputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
17 <help>
6
cabceaa239e4 planemo upload
jjjjia
parents: 5
diff changeset
18 clustalw2 -tree -infile=$input -outputtree=nj
1
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
19 </help>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
20 <citations>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
21 <citation type="bibtex">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
22 @misc{githubmob-suite,
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
23 author = {Robertson J, Nash J},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
24 title = {MOB-Suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
25 publisher = {GitHub},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
26 journal = {GitHub repository},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
27 doi = {10.1099/mgen.0.000206},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
28 url = {https://github.com/phac-nml/mob-suite}
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
29 }</citation>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
30 </citations>
6
cabceaa239e4 planemo upload
jjjjia
parents: 5
diff changeset
31 </tool>