Mercurial > repos > iss > eurl_vtec_wgs_pt
diff eurl_vtec_wgs_pt.xml @ 0:c6bab5103a14 draft
"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
| author | iss |
|---|---|
| date | Mon, 21 Mar 2022 15:23:09 +0000 |
| parents | |
| children | 444b0421bbdc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/eurl_vtec_wgs_pt.xml Mon Mar 21 15:23:09 2022 +0000 @@ -0,0 +1,217 @@ +<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="2.19">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 --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>