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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Tue, 28 Jan 2020 10:42:31 -0500
parents 6837f733b4aa
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2:6837f733b4aa 3:0cbed1c0a762
1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="2.3"> 1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="3.0">
2 <description>performs various typing tools test cfsan 2 <description>performs various typing tools</description>
3 </description>
4 <requirements> 3 <requirements>
5 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="3.7">python</requirement>
6 <requirement type="package">scipy</requirement> 5 <requirement type="package" version="5.26">perl</requirement>
7 <requirement type="package">perl-bioperl</requirement> 6 <requirement type="package">perl-bioperl</requirement>
8 <requirement type="package" version="2.3.5">bowtie2</requirement> 7 <requirement type="package" version="2.3.5">bowtie2</requirement>
9 <requirement type="package" version="1.3.1">samtools</requirement> 8 <requirement type="package" version="1.3.1">samtools</requirement>
10 <requirement type="package" version="1.3.1">bcftools</requirement> 9 <requirement type="package" version="1.3.1">bcftools</requirement>
11 <requirement type="package">bwa</requirement> 10 <requirement type="package">bwa</requirement>
12 <requirement type="package">blast</requirement> 11 <requirement type="package">mmseqs2</requirement>
13 <requirement type="package">spades</requirement> 12 <requirement type="package">spades</requirement>
14 <requirement type="package">fastqc</requirement> 13 <requirement type="package">fastqc</requirement>
15 <requirement type="package">mentalist</requirement> 14 <requirement type="package" version="0.2.4">mentalist</requirement>
15 <requirement type="package" version="3.6.7">ncbi-amrfinderplus</requirement>
16 </requirements> 16 </requirements>
17 <!-- basic error handling --> 17 <!-- basic error handling -->
18 <stdio> 18 <stdio>
19 <exit_code range="1:" level="fatal" description="Tool exception" /> 19 <exit_code range="1:" level="fatal" description="Tool exception" />
20 </stdio> 20 </stdio>
22 python 22 python
23 $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --mlstsevenloci $mlstsevenloci 23 $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --mlstsevenloci $mlstsevenloci
24 #if str( $library.type ) == "single": 24 #if str( $library.type ) == "single":
25 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' 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} 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 27 --text1 $text_file_1
28 #elif str( $library.type ) == "paired": 28 #elif str( $library.type ) == "paired":
29 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}' 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} 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 31 --text1 $text_file_1
32 -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}' 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} 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 34 --text2 $text_file_2
35 #elif str( $library.type ) == "pairedcollection": 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}' 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} 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 38 --text1 $text_file_1
39 -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}' 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} 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 41 --text2 $text_file_2
42 #end if 42 #end if
43 #if $serotyping: 43 #if $serotyping:
44 --serotyping 44 --serotyping
45 --spades_log $spades_log --blastn_O $blastn_O --blastn_H $blastn_H 45 --antigen_O $antigen_O --antigen_H $antigen_H
46 #end if 46 #end if
47 #if $virulotyping: 47 #if $virulotyping:
48 --virulotyping 48 --virulotyping
49 --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id) 49 --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id)
50 #end if 50 #end if
51 #if $shigatoxintyping: 51 #if $shigatoxintyping:
52 --shigatoxintyping 52 --shigatoxintyping
53 --blastn_STX $blastn_STX 53 --stx $stx
54 #end if
55 #if $amrtyping:
56 --amrtyping
57 --amr $amr
58 --amr_id $__app__.security.encode_id($amr.dataset.id)
54 #end if 59 #end if
55 </command> 60 </command>
56 61
57 <inputs> 62 <inputs>
58 <!-- single/paired --> 63 <!-- single/paired -->
74 </when> 79 </when>
75 </conditional> 80 </conditional>
76 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" /> 81 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" />
77 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" /> 82 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" />
78 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" /> 83 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" />
84 <param name="amrtyping" type="boolean" checked="true" label="Perform AMR typing" help="" />
79 </inputs> 85 </inputs>
80 86
81 <!-- define outputs --> 87 <!-- define outputs -->
82 <outputs> 88 <outputs>
83 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" /> 89 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" />
86 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> 92 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
87 </data> 93 </data>
88 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true"> 94 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true">
89 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter> 95 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
90 </data> 96 </data>
91 <data name="trimmed1" format="fastqsanger" label="${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 ${on_string}: log" /> 97 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
104 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}: Mapping reads" hidden="true"> 98 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}" hidden="true">
105 <filter>virulotyping</filter> 99 <filter>virulotyping</filter>
106 </data> 100 </data>
107 <data name="blastn_STX" format="tabular" label="Blastn for Shiga toxin on ${on_string}" hidden="true" > 101 <data name="stx" format="tabular" label="Shiga toxin subtyper on ${on_string}" hidden="true" >
108 <filter>shigatoxintyping</filter> 102 <filter>shigatoxintyping</filter>
109 </data> 103 </data>
110 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}: Alleles Table" hidden="true" /> 104 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}" hidden="true" />
111 <data name="spades_log" format="txt" label="SPAdes log" hidden="true"> 105 <data name="antigen_O" format="tabular" label="Antigen_O typer on ${on_string}" hidden="true">
112 <filter>serotyping</filter> 106 <filter>serotyping</filter>
113 </data> 107 </data>
114 <data name="blastn_O" format="tabular" label="Blastn for O on ${on_string}" hidden="true"> 108 <data name="antigen_H" format="tabular" label="Antigen_H typer on ${on_string}" hidden="true">
115 <filter>serotyping</filter> 109 <filter>serotyping</filter>
116 </data> 110 </data>
117 <data name="blastn_H" format="tabular" label="Blastn for H on ${on_string}" hidden="true"> 111 <data name="amr" format="tabular" label="AMR typer on ${on_string}" hidden="true">
118 <filter>serotyping</filter> 112 <filter>amrtyping</filter>
119 </data> 113 </data>
120 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data> 114 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
121 </outputs> 115 </outputs>
122 116
123 <tests> 117 <tests>
132 <has_text text="wzy_192_AF529080_O26" /> 126 <has_text text="wzy_192_AF529080_O26" />
133 <has_text text="fliC_269_AY337465_H11" /> 127 <has_text text="fliC_269_AY337465_H11" />
134 <has_text text="fliC_276_AY337472_H11" /> 128 <has_text text="fliC_276_AY337472_H11" />
135 </assert_contents> 129 </assert_contents>
136 </output> 130 </output>
137 <output name="blastn_O" file="blastn_O" ftype="tabular" /> 131 <output name="antigen_O" file="antigen_O" ftype="tabular" />
138 <output name="blastn_H" file="blastn_H" ftype="tabular" /> 132 <output name="antigen_H" file="antigen_H" ftype="tabular" />
139 </test> 133 </test>
140 </tests> 134 </tests>
141 135
142 <help> 136 <help>
143 **EURL VTEC WGS PT Overview** 137 **EURL VTEC WGS PT Overview**
145 139
146 - Raw data quality check (FASTQC) 140 - Raw data quality check (FASTQC)
147 141
148 - Trimming (FASTQ positional and quality trimming) 142 - Trimming (FASTQ positional and quality trimming)
149 143
144 - Assembly (SPAdes)
145
150 - Virulotyping (patho_typing tool from the INNUENDO Project) 146 - Virulotyping (patho_typing tool from the INNUENDO Project)
151 147
152 - Multi Locus Sequence Typing (MentaLiST 7 loci) 148 - Multi Locus Sequence Typing (MentaLiST 7 loci)
153 149
154 - Filtering (DUK) 150 - Serotyping (mmseqs2)
155 151
156 - Assembly (SPAdes) 152 - Shigatoxintyping (mmseqs2 against the shiga toxin subtype database from the Statens Serum Institut SSI and Technical University of Denmark DTU)
157 153
158 - Serotyping (blastn) 154 - AMR typing (AMRFinderPlus)
159
160 - Shigatoxintyping (blastn against the shiga toxin subtype database from the Statens Serum Institut (SSI) and Technical University of Denmark DTU)
161 155
162 Istituto Superiore di Sanità 156 Istituto Superiore di Sanità
163 157
164 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC) 158 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
165 159
179 }</citation> 173 }</citation>
180 <citation type="doi">10.1093/bioinformatics/btu135</citation> 174 <citation type="doi">10.1093/bioinformatics/btu135</citation>
181 <citation type="doi">10.1186/gb-2009-10-3-r25</citation> 175 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
182 <citation type="doi">10.1038/nmeth.1923</citation> 176 <citation type="doi">10.1038/nmeth.1923</citation>
183 <citation type="doi">10.1099/mgen.0.000146</citation> 177 <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> 178 <citation type="doi">10.1089/cmb.2012.0021</citation>
197 <citation type="doi">10.1186/1471-2105-10-421</citation> 179 <citation type="doi">10.1038/s41467-018-04964-5</citation>
198 <citation type="doi">10.1186/s13742-015-0080-7</citation> 180 <citation type="doi">10.1128/AAC.00483-19</citation>
199 <citation type="doi">10.1128/JCM.00008-15</citation> 181 <citation type="doi">10.1128/JCM.00008-15</citation>
200 </citations> 182 </citations>
201 </tool> 183 </tool>