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1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="4.0">
2 <description>workflow that performs various E. coli typing tools</description>
3 <requirements>
4 <requirement type="package" version="3.7">python</requirement>
5 <requirement type="package" version="5.26">perl</requirement>
6 <requirement type="package" version="1.7">perl-bioperl</requirement>
7 <requirement type="package" version="0.39">trimmomatic</requirement>
8 <requirement type="package" version="8.25">coreutils</requirement>
9 <requirement type="package" version="2.3.4">bowtie2</requirement>
10 <requirement type="package" version="1.3.1">samtools</requirement>
11 <requirement type="package" version="1.3.1">bcftools</requirement>
12 <requirement type="package" version="0.7.17">bwa</requirement>
13 <requirement type="package" version="3.15">spades</requirement>
14 <requirement type="package" version="2.3">skesa</requirement>
15 <requirement type="package" version="0.11.9">fastqc</requirement>
16 <requirement type="package" version="5.0.2">quast</requirement>
17 <requirement type="package" version="3.8">muscle</requirement>
18 <requirement type="package" version="2.19">mlst</requirement>
19 <requirement type="package" version="1.0.1">abricate</requirement>
20 <requirement type="package" version="2020.2">tbb</requirement>
21 </requirements>
22 <!-- basic error handling -->
23 <stdio>
24 <exit_code range="1:" level="fatal" description="Tool exception" />
25 </stdio>
26 <command>
27 <![CDATA[
28 python
29 $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --contigs $contigs --quast $quast --mlstsevenloci $mlstsevenloci
30 #if str( $library.type ) == "single":
31 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
32 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
33 --text1 $text_file_1
34 #elif str( $library.type ) == "paired":
35 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
36 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
37 --text1 $text_file_1
38 -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}'
39 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
40 --text2 $text_file_2
41 #elif str( $library.type ) == "pairedcollection":
42 -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}'
43 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
44 --text1 $text_file_1
45 -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}'
46 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
47 --text2 $text_file_2
48 #end if
49 #if $serotyping:
50 --serotyping
51 --antigen_O $antigen_O --antigen_H $antigen_H
52 #end if
53 #if $virulotyping:
54 --virulotyping
55 --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id)
56 #end if
57 #if $shigatoxintyping:
58 --shigatoxintyping
59 --stx $stx
60 #end if
61 #if $amrtyping:
62 --amrtyping
63 --amr $amr
64 --amr_id $__app__.security.encode_id($amr.dataset.id)
65 #end if
66 ]]>
67 </command>
68
69 <inputs>
70 <!-- single/paired -->
71 <conditional name="library">
72 <param name="type" type="select" label="Is this a single-end or paired-end library">
73 <option value="single">Single-end</option>
74 <option value="paired">Paired-end</option>
75 <option value="pairedcollection">Paired-end collection</option>
76 </param>
77 <when value="single">
78 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
79 </when>
80 <when value="paired">
81 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
82 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
83 </when>
84 <when value="pairedcollection">
85 <param name="input_pc" type="data_collection" label="Paired-end FASTQ collection" help="Must be of datatype &quot;fastqsanger&quot;" optional="false" format="txt" collection_type="paired" />
86 </when>
87 </conditional>
88 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" />
89 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" />
90 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" />
91 <param name="amrtyping" type="boolean" checked="true" label="Perform AMR typing" help="" />
92 </inputs>
93
94 <!-- define outputs -->
95 <outputs>
96 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" />
97 <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" />
98 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
99 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
100 </data>
101 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true">
102 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
103 </data>
104 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: contigs" />
105 <data format="tsv" name="quast" label="Quast on ${on_string}" hidden="true" />
106 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}" hidden="true">
107 <filter>virulotyping</filter>
108 </data>
109 <data name="stx" format="tabular" label="Shiga toxin subtyper on ${on_string}" hidden="true" >
110 <filter>shigatoxintyping</filter>
111 </data>
112 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}" hidden="true" />
113 <data name="antigen_O" format="tabular" label="Antigen_O typer on ${on_string}" hidden="true">
114 <filter>serotyping</filter>
115 </data>
116 <data name="antigen_H" format="tabular" label="Antigen_H typer on ${on_string}" hidden="true">
117 <filter>serotyping</filter>
118 </data>
119 <data name="amr" format="tabular" label="AMR typer on ${on_string}" hidden="true">
120 <filter>amrtyping</filter>
121 </data>
122 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
123 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
124 </outputs>
125
126 <tests>
127 <test>
128 <!-- basic test on contigs file -->
129 <param name="type" value="single"/>
130 <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/>
131 <param name="serotyping" value="true"/>
132 <output name="report_out">
133 <assert_contents>
134 <has_text text="wzx_208_AF529080_O26" />
135 <has_text text="wzy_192_AF529080_O26" />
136 <has_text text="fliC_269_AY337465_H11" />
137 <has_text text="fliC_276_AY337472_H11" />
138 </assert_contents>
139 </output>
140 <output name="antigen_O" file="antigen_O" ftype="tabular" />
141 <output name="antigen_H" file="antigen_H" ftype="tabular" />
142 </test>
143 </tests>
144
145 <help>
146 **EURL VTEC WGS PT Overview**
147 This tool performs various typing tools:
148
149 - Raw data quality check (FASTQC)
150
151 - Trimming (Trimmomatic)
152
153 - Assembly (SPAdes)
154
155 - Virulotyping (patho_typing tool from the INNUENDO Project)
156
157 - Multi Locus Sequence Typing (MLST 7 loci)
158
159 - Serotyping (blastn)
160
161 - Shigatoxintyping (blastn of a consensus sequence against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU)
162
163 - AMR typing (Abricate with ResFinder database)
164
165 Istituto Superiore di Sanità
166
167 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
168
169 Developer: Arnold Knijn arnold.knijn@iss.it
170
171 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
172 ("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”
173 from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014)
174 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
175 </help>
176 <citations>
177 <citation type="bibtex">@ARTICLE{andrews_s,
178 author = {Andrews, S},
179 keywords = {bioinformatics, ngs, qc},
180 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
181 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
182 }</citation>
183 <citation type="doi">10.1093/bioinformatics/btu170</citation>
184 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
185 <citation type="doi">10.1038/nmeth.1923</citation>
186 <citation type="bibtex">@ARTICLE{seemann_t,
187 author = {Seemann, T},
188 keywords = {bioinformatics, ngs},
189 title = {{mlst}},
190 url = {https://github.com/tseemann/mlst/}
191 }</citation>
192 <citation type="bibtex">@ARTICLE{seemann_t,
193 author = {Seemann, T},
194 keywords = {bioinformatics, ngs},
195 title = {{abricate}},
196 url = {https://github.com/tseemann/abricate/}
197 }</citation>
198 <citation type="doi">10.1089/cmb.2012.0021</citation>
199 <citation type="doi">10.1186/s13059-018-1540-z</citation>
200 <citation type="doi">d10.1093/jac/dks261</citation>
201 <citation type="doi">10.1128/JCM.00008-15</citation>
202 <citation type="bibtex">@ARTICLE{andrews_s,
203 author = {Li, M, Copeland, A, and Han, J},
204 keywords = {bioinformatics, ngs},
205 title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
206 url = {https://www.osti.gov/servlets/purl/1016000/}
207 }</citation>
208 <citation type="bibtex">@ARTICLE{andrews_s,
209 author = {Edwards, RA},
210 keywords = {bioinformatics, ngs},
211 title = {{fastq-pair}},
212 url = {https://github.com/linsalrob/EdwardsLab/}
213 }</citation>
214 <citation type="doi">10.1186/1471-2105-10-421</citation>
215 <citation type="doi">10.1093/nar/gkh340</citation>
216 </citations>
217 </tool>