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date Wed, 22 Jan 2020 08:41:44 -0500
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1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="2.3">
2 <description>performs various typing tools
3 </description>
4 <requirements>
5 <requirement type="package" version="2.7">python</requirement>
6 <requirement type="package">scipy</requirement>
7 <requirement type="package">perl-bioperl</requirement>
8 <requirement type="package" version="2.2.9">bowtie2</requirement>
9 <requirement type="package" version="1.3.1">samtools</requirement>
10 <requirement type="package" version="1.3.1">bcftools</requirement>
11 <requirement type="package">bwa</requirement>
12 <requirement type="package">blast</requirement>
13 <requirement type="package">spades</requirement>
14 <requirement type="package">fastqc</requirement>
15 <requirement type="package">mentalist</requirement>
16 </requirements>
17 <!-- basic error handling -->
18 <stdio>
19 <exit_code range="1:" level="fatal" description="Tool exception" />
20 </stdio>
21 <command>
22 python
23 $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --mlstsevenloci $mlstsevenloci
24 #if str( $library.type ) == "single":
25 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
26 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
27 --text1 $text_file_1 --trimmed1 $trimmed1
28 #elif str( $library.type ) == "paired":
29 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
30 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
31 --text1 $text_file_1 --trimmed1 $trimmed1
32 -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}'
33 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
34 --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
35 #elif str( $library.type ) == "pairedcollection":
36 -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}'
37 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
38 --text1 $text_file_1 --trimmed1 $trimmed1
39 -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}'
40 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
41 --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
42 #end if
43 #if $serotyping:
44 --serotyping
45 --spades_log $spades_log --blastn_O $blastn_O --blastn_H $blastn_H
46 #end if
47 #if $virulotyping:
48 --virulotyping
49 --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id)
50 #end if
51 #if $shigatoxintyping:
52 --shigatoxintyping
53 --blastn_STX $blastn_STX
54 #end if
55 </command>
56
57 <inputs>
58 <!-- single/paired -->
59 <conditional name="library">
60 <param name="type" type="select" label="Is this a single-end or paired-end library">
61 <option value="single">Single-end</option>
62 <option value="paired">Paired-end</option>
63 <option value="pairedcollection">Paired-end collection</option>
64 </param>
65 <when value="single">
66 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
67 </when>
68 <when value="paired">
69 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
70 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
71 </when>
72 <when value="pairedcollection">
73 <param name="input_pc" type="data_collection" label="Paired-end FASTQ collection" help="Must be of datatype &quot;fastqsanger&quot;" optional="false" format="txt" collection_type="paired" />
74 </when>
75 </conditional>
76 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" />
77 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" />
78 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" />
79 </inputs>
80
81 <!-- define outputs -->
82 <outputs>
83 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" />
84 <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" />
85 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
86 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
87 </data>
88 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true">
89 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
90 </data>
91 <data name="trimmed1" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed
92 #if str( $library.type ) == 'paired'#
93 forward
94 #end if#
95 FASTQ">
96 </data>
97 <data name="trimmed2" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed reverse FASTQ">
98 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
99 </data>
100 <data name="trimmedunpaired" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed unpaired reads">
101 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
102 </data>
103 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
104 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}: Mapping reads" hidden="true">
105 <filter>virulotyping</filter>
106 </data>
107 <data name="blastn_STX" format="tabular" label="Blastn for Shiga toxin on ${on_string}" hidden="true" >
108 <filter>shigatoxintyping</filter>
109 </data>
110 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}: Alleles Table" hidden="true" />
111 <data name="spades_log" format="txt" label="SPAdes log" hidden="true">
112 <filter>serotyping</filter>
113 </data>
114 <data name="blastn_O" format="tabular" label="Blastn for O on ${on_string}" hidden="true">
115 <filter>serotyping</filter>
116 </data>
117 <data name="blastn_H" format="tabular" label="Blastn for H on ${on_string}" hidden="true">
118 <filter>serotyping</filter>
119 </data>
120 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
121 </outputs>
122
123 <tests>
124 <test>
125 <!-- basic test on contigs file -->
126 <param name="type" value="single"/>
127 <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/>
128 <param name="serotyping" value="true"/>
129 <output name="report_out">
130 <assert_contents>
131 <has_text text="wzx_208_AF529080_O26" />
132 <has_text text="wzy_192_AF529080_O26" />
133 <has_text text="fliC_269_AY337465_H11" />
134 <has_text text="fliC_276_AY337472_H11" />
135 </assert_contents>
136 </output>
137 <output name="blastn_O" file="blastn_O" ftype="tabular" />
138 <output name="blastn_H" file="blastn_H" ftype="tabular" />
139 </test>
140 </tests>
141
142 <help>
143 **EURL VTEC WGS PT Overview**
144 This tool performs various typing tools:
145
146 - Raw data quality check (FASTQC)
147
148 - Trimming (FASTQ positional and quality trimming)
149
150 - Virulotyping (patho_typing tool from the INNUENDO Project)
151
152 - Multi Locus Sequence Typing (MentaLiST 7 loci)
153
154 - Filtering (DUK)
155
156 - Assembly (SPAdes)
157
158 - Serotyping (blastn)
159
160 - Shigatoxintyping (blastn against the shiga toxin subtype database from the Statens Serum Institut (SSI) and Technical University of Denmark DTU)
161
162 Istituto Superiore di Sanità
163
164 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
165
166 Developer: Arnold Knijn arnold.knijn@iss.it
167
168 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
169 ("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”
170 from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014)
171 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
172 </help>
173 <citations>
174 <citation type="bibtex">@ARTICLE{andrews_s,
175 author = {Andrews, S},
176 keywords = {bioinformatics, ngs, qc},
177 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
178 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
179 }</citation>
180 <citation type="doi">10.1093/bioinformatics/btu135</citation>
181 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
182 <citation type="doi">10.1038/nmeth.1923</citation>
183 <citation type="doi">10.1099/mgen.0.000146</citation>
184 <citation type="bibtex">@ARTICLE{li-copeland,
185 author = {Li, M, Copeland, A, and Han, J},
186 keywords = {bioinformatics, ngs},
187 title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
188 url = {https://www.osti.gov/servlets/purl/1016000/}
189 }</citation>
190 <citation type="bibtex">@ARTICLE{edwards_ra,
191 author = {Edwards, RA},
192 keywords = {bioinformatics, ngs},
193 title = {{fastq-pair}},
194 url = {https://github.com/linsalrob/EdwardsLab/}
195 }</citation>
196 <citation type="doi">10.1089/cmb.2012.0021</citation>
197 <citation type="doi">10.1186/1471-2105-10-421</citation>
198 <citation type="doi">10.1186/s13742-015-0080-7</citation>
199 <citation type="doi">10.1128/JCM.00008-15</citation>
200 </citations>
201 </tool>