Next changeset 1:579f1cabfe79 (2022-03-09) |
Commit message:
"planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275" |
added:
legsta.xml macros.xml test-data/NC_006368.fna.bz2 |
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diff -r 000000000000 -r b469f6d53d06 legsta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/legsta.xml Mon Feb 21 20:23:38 2022 +0000 |
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@@ -0,0 +1,66 @@ +<tool id="legsta" name="legsta" version="@TOOL_VERSION@" profile="20.01"> + <description>Legionella pneumophila sequence based typing</description> + + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + + <command detect_errors="exit_code"><![CDATA[ + legsta + + $noheader + $csv + + #for $i in $contigs + '$i' + #end for + + > '$output' + ]]></command> + + <inputs> + <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." /> + <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 ...)" /> + <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." /> + </inputs> + + <outputs> + <data name="output" format="tabular"> + <change_format> + <when input="csv" value="--csv" format="csv" /> + <when input="csv" value="" format="tabular" /> + </change_format> + </data> + </outputs> + + <tests> + <test> + <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/> + <param name="csv" value="true"/> + <output name="output"> + <assert_contents> + <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" /> + <has_text text="1,1,4,3,1,1,1,1" /> + </assert_contents> + </output> + </test> + </tests> + + <help> +In silico sequence based typing (SBT) of Legionella pneumophila. + +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. + </help> + + <citations> + <citation type="bibtex"> +@misc{githublegsta, + author = {Seemann, Torsten and Da Silva, Anders Goncalves, and Buultjens, Andrew, and Kwong, Jason}, + title = {legsta}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/tseemann/legsta}, +}</citation> + </citations> +</tool> |
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diff -r 000000000000 -r b469f6d53d06 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Feb 21 20:23:38 2022 +0000 |
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@@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">legsta</requirement> + </requirements> + </xml> + <token name="@TOOL_VERSION@">0.5.1</token> +</macros> |
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diff -r 000000000000 -r b469f6d53d06 test-data/NC_006368.fna.bz2 |
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Binary file test-data/NC_006368.fna.bz2 has changed |