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<tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="4.0"> <description>workflow that performs various E. coli typing tools</description> <requirements> <requirement type="package" version="3.7">python</requirement> <requirement type="package" version="5.26">perl</requirement> <requirement type="package" version="1.7">perl-bioperl</requirement> <requirement type="package" version="0.39">trimmomatic</requirement> <requirement type="package" version="8.25">coreutils</requirement> <requirement type="package" version="2.3.4">bowtie2</requirement> <requirement type="package" version="1.3.1">samtools</requirement> <requirement type="package" version="1.3.1">bcftools</requirement> <requirement type="package" version="0.7.17">bwa</requirement> <requirement type="package" version="3.15">spades</requirement> <requirement type="package" version="2.3">skesa</requirement> <requirement type="package" version="0.11.9">fastqc</requirement> <requirement type="package" version="5.0.2">quast</requirement> <requirement type="package" version="3.8">muscle</requirement> <requirement type="package" version="2.23">mlst</requirement> <requirement type="package" version="1.0.1">abricate</requirement> <requirement type="package" version="2020.2">tbb</requirement> </requirements> <!-- basic error handling --> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command> <![CDATA[ python $__tool_directory__/EURL_VTEC_WGS_PT.py --base_url $__app__.config.galaxy_infrastructure_url --log $logfile --output $report_out --contigs $contigs --quast $quast --mlstsevenloci $mlstsevenloci #if str( $library.type ) == "single": -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} --text1 $text_file_1 #elif str( $library.type ) == "paired": -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} --text1 $text_file_1 -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}' --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} --text2 $text_file_2 #elif str( $library.type ) == "pairedcollection": -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}' --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path} --text1 $text_file_1 -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}' --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path} --text2 $text_file_2 #end if #if $serotyping: --serotyping --antigen_O $antigen_O --antigen_H $antigen_H #end if #if $virulotyping: --virulotyping --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id) #end if #if $shigatoxintyping: --shigatoxintyping --stx $stx #end if #if $amrtyping: --amrtyping --amr $amr --amr_id $__app__.security.encode_id($amr.dataset.id) #end if ]]> </command> <inputs> <!-- single/paired --> <conditional name="library"> <param name="type" type="select" label="Is this a single-end or paired-end library"> <option value="single">Single-end</option> <option value="paired">Paired-end</option> <option value="pairedcollection">Paired-end collection</option> </param> <when value="single"> <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype "fastqsanger"" /> </when> <when value="paired"> <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> </when> <when value="pairedcollection"> <param name="input_pc" type="data_collection" label="Paired-end FASTQ collection" help="Must be of datatype "fastqsanger"" optional="false" format="txt" collection_type="paired" /> </when> </conditional> <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" /> <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" /> <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" /> <param name="amrtyping" type="boolean" checked="true" label="Perform AMR typing" help="" /> </inputs> <!-- define outputs --> <outputs> <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" /> <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" /> <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true"> <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> </data> <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true"> <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> </data> <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: contigs" /> <data format="tsv" name="quast" label="Quast on ${on_string}" hidden="true" /> <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}" hidden="true"> <filter>virulotyping</filter> </data> <data name="stx" format="tabular" label="Shiga toxin subtyper on ${on_string}" hidden="true" > <filter>shigatoxintyping</filter> </data> <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}" hidden="true" /> <data name="antigen_O" format="tabular" label="Antigen_O typer on ${on_string}" hidden="true"> <filter>serotyping</filter> </data> <data name="antigen_H" format="tabular" label="Antigen_H typer on ${on_string}" hidden="true"> <filter>serotyping</filter> </data> <data name="amr" format="tabular" label="AMR typer on ${on_string}" hidden="true"> <filter>amrtyping</filter> </data> <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" /> <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data> </outputs> <tests> <test> <!-- basic test on contigs file --> <param name="type" value="single"/> <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/> <param name="serotyping" value="true"/> <output name="report_out"> <assert_contents> <has_text text="wzx_208_AF529080_O26" /> <has_text text="wzy_192_AF529080_O26" /> <has_text text="fliC_269_AY337465_H11" /> <has_text text="fliC_276_AY337472_H11" /> </assert_contents> </output> <output name="antigen_O" file="antigen_O" ftype="tabular" /> <output name="antigen_H" file="antigen_H" ftype="tabular" /> </test> </tests> <help> **EURL VTEC WGS PT Overview** This tool performs various typing tools: - Raw data quality check (FASTQC) - Trimming (Trimmomatic) - Assembly (SPAdes) - Virulotyping (patho_typing tool from the INNUENDO Project) - Multi Locus Sequence Typing (MLST 7 loci) - Serotyping (blastn) - Shigatoxintyping (blastn of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU) - AMR typing (Abricate with ResFinder database) Istituto Superiore di Sanità European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC) Developer: Arnold Knijn arnold.knijn@iss.it The development of the Virulotyping tool has been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2 ("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento” from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014) [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)]. </help> <citations> <citation type="bibtex">@ARTICLE{andrews_s, author = {Andrews, S}, keywords = {bioinformatics, ngs, qc}, title = {{FastQC A Quality Control tool for High Throughput Sequence Data}}, url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/} }</citation> <citation type="doi">10.1093/bioinformatics/btu170</citation> <citation type="doi">10.1186/gb-2009-10-3-r25</citation> <citation type="doi">10.1038/nmeth.1923</citation> <citation type="bibtex">@ARTICLE{seemann_t, author = {Seemann, T}, keywords = {bioinformatics, ngs}, title = {{mlst}}, url = {https://github.com/tseemann/mlst/} }</citation> <citation type="bibtex">@ARTICLE{seemann_t, author = {Seemann, T}, keywords = {bioinformatics, ngs}, title = {{abricate}}, url = {https://github.com/tseemann/abricate/} }</citation> <citation type="doi">10.1089/cmb.2012.0021</citation> <citation type="doi">10.1186/s13059-018-1540-z</citation> <citation type="doi">d10.1093/jac/dks261</citation> <citation type="doi">10.1128/JCM.00008-15</citation> <citation type="bibtex">@ARTICLE{andrews_s, author = {Li, M, Copeland, A, and Han, J}, keywords = {bioinformatics, ngs}, title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}}, url = {https://www.osti.gov/servlets/purl/1016000/} }</citation> <citation type="bibtex">@ARTICLE{andrews_s, author = {Edwards, RA}, keywords = {bioinformatics, ngs}, title = {{fastq-pair}}, url = {https://github.com/linsalrob/EdwardsLab/} }</citation> <citation type="doi">10.1186/1471-2105-10-421</citation> <citation type="doi">10.1093/nar/gkh340</citation> </citations> </tool>