Mercurial > repos > iuc > legsta

annotate legsta.xml @ 1:579f1cabfe79 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
author iuc
date Wed, 09 Mar 2022 20:49:51 +0000
parents b469f6d53d06
children 0411fca1d681
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
1 <tool id="legsta" name="legsta" version="@TOOL_VERSION@+galaxy1" profile="20.01">
0
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
2 <description>Legionella pneumophila sequence based typing</description>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
3
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
4 <macros>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
5 <import>macros.xml</import>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
6 </macros>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
8
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
1
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
10 #import re
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
11 #set safe_names=[]
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
12
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
13 #for $i in $contigs
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
14 #set safe_name=re.sub('[^\s\w\-.]', '_', str($i.element_identifier))
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
15 $safe_names.append($safe_name)
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
16 ln -s '$i' '$safe_name';
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
17 #end for
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
18
0
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
19 legsta
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
20
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
21 $noheader
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
22 $csv
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
23
1
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
24 #for $safe_name in $safe_names
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
25 '$safe_name'
0
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
26 #end for
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
27
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
28 > '$output'
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
29 ]]></command>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
30
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
31 <inputs>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
32 <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." />
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
33 <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 ...)" />
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
34 <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." />
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
35 </inputs>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
36
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
37 <outputs>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
38 <data name="output" format="tabular">
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
39 <change_format>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
40 <when input="csv" value="--csv" format="csv" />
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
41 <when input="csv" value="" format="tabular" />
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
42 </change_format>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
43 </data>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
44 </outputs>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
45
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
46 <tests>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
47 <test>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
48 <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
49 <param name="csv" value="true"/>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
50 <output name="output">
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
51 <assert_contents>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
52 <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
1
579f1cabfe79 "planemo upload for repository https://github.com/tseemann/legsta commit 4e41978ca2530441bd5abf07a37ab9e8eedfce6c"
iuc
parents: 0
diff changeset
53 <has_text text="NC_006368.fna.bz2,1,1,4,3,1,1,1,1" />
0
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
54 </assert_contents>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
55 </output>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
56 </test>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
57 </tests>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
58
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
59 <help>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
60 In silico sequence based typing (SBT) of Legionella pneumophila.
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
61
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
62 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.
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
63 </help>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
64
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
65 <citations>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
66 <citation type="bibtex">
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
67 @misc{githublegsta,
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
68 author = {Seemann, Torsten and Da Silva, Anders Goncalves, and Buultjens, Andrew, and Kwong, Jason},
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
69 title = {legsta},
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
70 publisher = {GitHub},
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
71 journal = {GitHub repository},
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
72 url = {https://github.com/tseemann/legsta},
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
73 }</citation>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
74 </citations>
b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
iuc
parents:
diff changeset
75 </tool>