Mercurial > repos > iss > eurl_vtec_wgs_pt
comparison eurl_vtec_wgs_pt.xml @ 0:c6bab5103a14 draft
"planemo upload commit 6abf3e299d82d07e6c3cf8642bdea80e96df64c3-dirty"
author | iss |
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date | Mon, 21 Mar 2022 15:23:09 +0000 |
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children | 444b0421bbdc |
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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 "fastqsanger"" /> | |
79 </when> | |
80 <when value="paired"> | |
81 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype "fastqsanger"" /> | |
82 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype "fastqsanger"" /> | |
83 </when> | |
84 <when value="pairedcollection"> | |
85 <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" /> | |
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> |