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author dcouvin
date Mon, 06 Sep 2021 16:00:46 +0000
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1 <tool id="pmlst" name="pmlst" version="2.0+galaxy1">
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 <requirement type="package" version="2.7.1">blastn</requirement>
12 </requirements>
13
14
15 <!--<command> python3 $__tool_directory__/pmlst/pmlst.py -i $input -s $s -p $__tool_directory__/pmlst/pmlst_db/ > $output </command>-->
16
17 <!--<command> perl $__tool_directory__/pmlst.pl $__tool_directory__ $input $s > $output </command>-->
18
19 <command detect_errors="aggressive"><![CDATA[
20
21 #import re
22 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
23 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
24
25 ## Add single quotes around each input file identifier
26 #set $_input_file = "'{}'".format($input.element_identifier)
27 ln -s '${input}' ${_input_file} &&
28
29
30 perl $__tool_directory__/pmlst.pl $__tool_directory__ $_input_file $s > $output
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32
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34 ]]></command>
35
36 <inputs>
37 <param format="fasta" name="input" type="data" label="Select FASTA files: " />
38
39
40 <param name="s" type="select" label="Scheme database used for pMLST prediction:">
41
42 <option value="incac">incac</option>
43 <option value="incf">incf</option>
44 <option value="inchi1">inchi1</option>
45 <option value="inchi2">inchi2</option>
46 <option value="inci1">inci1</option>
47 <option value="incn">incn</option>
48 <option value="pbssb1-family">pbssb1-family</option>
49
50 </param>
51
52
53 </inputs>
54
55 <outputs>
56 <data format="tabular" name="output" />
57 </outputs>
58
59 <help>
60
61 </help>
62 <citations>
63 <citation type="doi">10.1007/978-1-4939-9877-7_20</citation>
64 </citations>
65 </tool>
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