Mercurial > repos > dcouvin > pmlst

comparison pmlst.xml @ 0:6dcb66689a7d draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author dcouvin
date Wed, 25 Aug 2021 21:12:34 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:6dcb66689a7d
1 <tool id="pmlst" name="pmlst" version="2.0">
2 <description>A plasmid multilocus sequence typing (pMLST) scheme was developed for rapid categorization of IncN plasmids</description>
3
4
5 <requirements>
6 <requirement type="package" version="3.2.0">python3-openid</requirement>
7 <requirement type="package" version="21.2.4">pip</requirement>
8 <requirement type="package" version="1.79">biopython</requirement>
9 <requirement type="package" version="1.5.6">cgecore</requirement>
10 <requirement type="package" version="0.8.9">tabulate</requirement>
11 </requirements>
12
13
14 <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output </command>-->
15
16 <command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command>
17
18 <inputs>
19 <param format="fasta" name="input" type="data" label="Select FASTA files: " />
20
21 <param name="s" type="select" label="Scheme database used for pMLST prediction:">
22
23 <option value="incac">incac</option>
24 <option value="incf">incf</option>
25 <option value="inchi1">inchi1</option>
26 <option value="inchi2">inchi2</option>
27 <option value="inci1">inci1</option>
28 <option value="incn">incn</option>
29 <option value="pbssb1-family">pbssb1-family</option>
30
31 </param>
32
33
34 </inputs>
35
36 <outputs>
37 <data format="tabular" name="output" />
38 </outputs>
39
40 <help>
41
42 </help>
43 <citations>
44 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
45 </citations>
46 </tool>
47
48
49