Mercurial > repos > iuc > abricate

annotate abricate_list.xml @ 1:3535be5366fc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
author iuc
date Fri, 03 Mar 2017 14:55:53 -0500
parents d9f706e77d5e
children c13e1b424711
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
1 <tool id="abricate_list" name="ABRicate List" version="0.3">
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
2 <requirements>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
3 <requirement type="package" version="0.3">abricate</requirement>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
4 </requirements>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
5
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
6 <version_command>abricate --version</version_command>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
7
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
1
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
9 abricate --list 2> '$report'
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
10 ]]></command>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
11
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
12 <inputs>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
13 </inputs>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
14
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
15 <outputs>
1
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
16 <data name="report" format="txt" label="${tool.name} - list of databases"/>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
17 </outputs>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
18
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
19 <tests>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
20 <test>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
21 <output name="report" ftype="txt" file="output_list.txt" />
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
22 </test>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
23 </tests>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
24
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
25 <help><![CDATA[
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
26 **What it does**
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
27
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
28 ABRicate List will list all the antibiotic databases used by ABRicate. The database of these genes is built from ResFinder.
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
29 ]]></help>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
30
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
31 <citations>
1
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
32 <citation type="bibtex">
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
33 @UNPUBLISHED{Seemann2016,
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
34 author = {Seemann, Torsten},
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
35 title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
36 year = {2016},
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
37 url = {https://github.com/tseemann/abricate},
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
38 }
3535be5366fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
iuc
parents: 0
diff changeset
39 </citation>
0
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
40 </citations>
d9f706e77d5e planemo upload commit f22cab0d69f28a0fd9e2043e4a77bb41e2e771f9
iuc
parents:
diff changeset
41 </tool>