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planemo upload for repository https://github.com/tseemann/legsta commit ba53da012895c122e1fb7576c68d18c1a70320b4
author iuc
date Tue, 12 Mar 2024 11:16:20 +0000
parents 579f1cabfe79
children
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0411fca1d681 planemo upload for repository https://github.com/tseemann/legsta commit ba53da012895c122e1fb7576c68d18c1a70320b4
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1 <tool id="legsta" name="legsta" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>Legionella pneumophila sequence based typing</description>
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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 <xrefs>
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8 <xref type="bio.tools">legsta</xref>
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9 </xrefs>
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10 <expand macro="requirements"/>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #import re
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14 #set safe_names=[]
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16 #for $i in $contigs
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17 #set safe_name=re.sub('[^\s\w\-.]', '_', str($i.element_identifier))
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18 $safe_names.append($safe_name)
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19 ln -s '$i' '$safe_name';
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20 #end for
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21
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22 legsta
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24 $noheader
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25 $csv
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26
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27 #for $safe_name in $safe_names
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28 '$safe_name'
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29 #end for
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31 > '$output'
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32 ]]></command>
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34 <inputs>
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35 <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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36 <param argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Remove table header" help="Removes the table header from the output (ie. FILE SBT flaA ...)" />
0411fca1d681 planemo upload for repository https://github.com/tseemann/legsta commit ba53da012895c122e1fb7576c68d18c1a70320b4
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37 <param argument="--csv" type="boolean" 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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38 </inputs>
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40 <outputs>
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41 <data name="output" format="tabular">
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42 <change_format>
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43 <when input="csv" value="--csv" format="csv" />
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44 </change_format>
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45 </data>
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46 </outputs>
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48 <tests>
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49 <test>
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50 <param name="contigs" ftype="fasta" value="NC_006368.fna.bz2"/>
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51 <param name="csv" value="true"/>
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52 <output name="output">
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53 <assert_contents>
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54 <has_text text="SBT,flaA,pilE,asd,mip,mompS,proA,neuA" />
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55 <has_text text="NC_006368.fna.bz2,1,1,4,3,1,1,1,1" />
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56 </assert_contents>
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57 </output>
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58 </test>
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59 </tests>
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61 <help>
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62 In silico sequence based typing (SBT) of Legionella pneumophila.
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63
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64 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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65 </help>
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66
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67 <citations>
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68 <citation type="bibtex">
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69 @misc{githublegsta,
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70 author = {Seemann, Torsten and Da Silva, Anders Goncalves, and Buultjens, Andrew, and Kwong, Jason},
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71 title = {legsta},
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72 publisher = {GitHub},
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73 journal = {GitHub repository},
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74 url = {https://github.com/tseemann/legsta},
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75 }</citation>
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76 </citations>
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77 </tool>