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annotate 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
parents
children 579f1cabfe79
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b469f6d53d06 "planemo upload for repository https://github.com/tseemann/legsta commit 19e59e87fedc1e6a85e946e3be15d165c16f4275"
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1 <tool id="legsta" name="legsta" version="@TOOL_VERSION@" profile="20.01">
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2 <description>Legionella pneumophila sequence based typing</description>
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3
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8
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9 <command detect_errors="exit_code"><![CDATA[
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10 legsta
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12 $noheader
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13 $csv
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14
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15 #for $i in $contigs
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16 '$i'
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17 #end for
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18
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19 > '$output'
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20 ]]></command>
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22 <inputs>
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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." />
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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 ...)" />
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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." />
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26 </inputs>
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28 <outputs>
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29 <data name="output" format="tabular">
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30 <change_format>
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31 <when input="csv" value="--csv" format="csv" />
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32 <when input="csv" value="" format="tabular" />
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33 </change_format>
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34 </data>
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35 </outputs>
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36
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37 <tests>
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38 <test>
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39 <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/>
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40 <param name="csv" value="true"/>
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41 <output name="output">
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42 <assert_contents>
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43 <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
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44 <has_text text="1,1,4,3,1,1,1,1" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 </tests>
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49
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50 <help>
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51 In silico sequence based typing (SBT) of Legionella pneumophila.
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52
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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.
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54 </help>
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55
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56 <citations>
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57 <citation type="bibtex">
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58 @misc{githublegsta,
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59 author = {Seemann, Torsten and Da Silva, Anders Goncalves, and Buultjens, Andrew, and Kwong, Jason},
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60 title = {legsta},
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61 publisher = {GitHub},
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62 journal = {GitHub repository},
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63 url = {https://github.com/tseemann/legsta},
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64 }</citation>
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65 </citations>
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66 </tool>