annotate cpo_resfinder.xml @ 9:e0ba039c1119 draft

planemo upload
author jjjjia
date Fri, 24 Aug 2018 14:10:07 -0400
parents 698579246d0d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
698579246d0d planemo upload
jjjjia
parents: 1
diff changeset
1 <tool id="cpo_resfinder" name="cpo_resfinder" version="0.8">
698579246d0d planemo upload
jjjjia
parents: 1
diff changeset
2 <description>Modified version of Resfinder 0.8 to use custom carbapenamase database</description>
1
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
3 <requirements>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
4 <requirement type="package" version="0.8">abricate</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[
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
8 abricate
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
9 --datadir=$__tool_directory__/
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
10 --db=cpo
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
11 '$input'
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
12 >report.tsv
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
13 ]]>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
14 </command>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
15 <inputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
16 <param type="data" name="input" format="fasta" />
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
17 </inputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
18 <outputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
19 <data name="report" format="tabular" from_work_dir="report.tsv"/>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
20 </outputs>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
21 <help>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
22 abricate with custom database
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
23 </help>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
24 <citations>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
25 <citation type="bibtex">
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
26 @misc{cpo,
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
27 author = {j, j},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
28 year = {2018},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
29 title = {cpo_prediction},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
30 publisher = {j},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
31 journal = {j of j},
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
32 url = {https://bfjia.net,
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
33 }</citation>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
34 </citations>
fea89c4d5227 Uploaded
jjjjia
parents:
diff changeset
35 </tool>