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comparison legsta.xml @ 0:b469f6d53d06 draft

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"planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
author iuc
date Mon, 21 Feb 2022 20:23:38 +0000
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-1:000000000000 0:b469f6d53d06
1 <tool id="legsta" name="legsta" version="@TOOL_VERSION@" profile="20.01">
2 <description>Legionella pneumophila sequence based typing</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8
9 <command detect_errors="exit_code"><![CDATA[
10 legsta
11
12 $noheader
13 $csv
14
15 #for $i in $contigs
16 '$i'
17 #end for
18
19 > '$output'
20 ]]></command>
21
22 <inputs>
23 <param type="data" name="contigs" format="genbank,embl,gff,gff3,fasta,fasta.gz,fastq,fastq.gz,clustal,stockholm" multiple="true" label="Contigs" help="One or more input files in FASTA, FASTQ, Genbank, EMBL, Clustal, Stockholm or GFF format." />
24 <param name="noheader" type="boolean" argument="--noheader" truevalue="--noheader" falsevalue="" label="Remove table header" help="Removes the table header from the output (ie. FILE SBT flaA ...)" />
25 <param name="csv" type="boolean" argument="--csv" truevalue="--csv" falsevalue="" label="CSV output" help="Prints the output in comma-separated value format instead of tab-separated value format." />
26 </inputs>
27
28 <outputs>
29 <data name="output" format="tabular">
30 <change_format>
31 <when input="csv" value="--csv" format="csv" />
32 <when input="csv" value="" format="tabular" />
33 </change_format>
34 </data>
35 </outputs>
36
37 <tests>
38 <test>
39 <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/>
40 <param name="csv" value="true"/>
41 <output name="output">
42 <assert_contents>
43 <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
44 <has_text text="1,1,4,3,1,1,1,1" />
45 </assert_contents>
46 </output>
47 </test>
48 </tests>
49
50 <help>
51 In silico sequence based typing (SBT) of Legionella pneumophila.
52
53 The purpose of the Legionella pneumophila SBT scheme is to provide a rapid and easily comparable method for the epidemiological typing of clinical and environmental isolates of Legionella pneumophila in outbreak investigations.
54 </help>
55
56 <citations>
57 <citation type="bibtex">
58 @misc{githublegsta,
59 author = {Seemann, Torsten and Da Silva, Anders Goncalves, and Buultjens, Andrew, and Kwong, Jason},
60 title = {legsta},
61 publisher = {GitHub},
62 journal = {GitHub repository},
63 url = {https://github.com/tseemann/legsta},
64 }</citation>
65 </citations>
66 </tool>