Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate eurl_vtec_wgs_pt.xml @ 1:bf3194a789a2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 08:45:40 -0500
parents 965517909457
children 6837f733b4aa
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
1 <tool id="eurlvtecwgspt" name="EURL VTEC WGS PT" version="2.3">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
2 <description>performs various typing tools
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
3 </description>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
4 <requirements>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
5 <requirement type="package" version="2.7">python</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
6 <requirement type="package">scipy</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
7 <requirement type="package">perl-bioperl</requirement>
1
bf3194a789a2 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents: 0
diff changeset
8 <requirement type="package" version="2.3.5">bowtie2</requirement>
0
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
9 <requirement type="package" version="1.3.1">samtools</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
10 <requirement type="package" version="1.3.1">bcftools</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
11 <requirement type="package">bwa</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
12 <requirement type="package">blast</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
13 <requirement type="package">spades</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
14 <requirement type="package">fastqc</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
15 <requirement type="package">mentalist</requirement>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
16 </requirements>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
17 <!-- basic error handling -->
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
18 <stdio>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
19 <exit_code range="1:" level="fatal" description="Tool exception" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
20 </stdio>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
21 <command>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
22 python
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
23 $__tool_directory__/EURL_VTEC_WGS_PT.py --log $logfile --output $report_out --mlstsevenloci $mlstsevenloci
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
24 #if str( $library.type ) == "single":
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
25 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
26 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
27 --text1 $text_file_1 --trimmed1 $trimmed1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
28 #elif str( $library.type ) == "paired":
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
29 -1 ${library.input_1} --input1_ext ${library.input_1.ext} --input1_name '${library.input_1.name}'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
30 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
31 --text1 $text_file_1 --trimmed1 $trimmed1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
32 -2 ${library.input_2} --input2_ext ${library.input_2.ext} --input2_name '${library.input_2.name}'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
33 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
34 --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
35 #elif str( $library.type ) == "pairedcollection":
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
36 -1 ${library.input_pc.forward} --input1_ext ${library.input_pc.forward.ext} --input1_name '${library.input_pc.forward.name}'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
37 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
38 --text1 $text_file_1 --trimmed1 $trimmed1
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
39 -2 ${library.input_pc.reverse} --input2_ext ${library.input_pc.reverse.ext} --input2_name '${library.input_pc.reverse.name}'
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
40 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
41 --text2 $text_file_2 --trimmed2 $trimmed2 --trimmedunpaired $trimmedunpaired
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
42 #end if
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
43 #if $serotyping:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
44 --serotyping
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
45 --spades_log $spades_log --blastn_O $blastn_O --blastn_H $blastn_H
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
46 #end if
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
47 #if $virulotyping:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
48 --virulotyping
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
49 --virulotyper $virulotyper --virulotyper_id $__app__.security.encode_id($virulotyper.dataset.id)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
50 #end if
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
51 #if $shigatoxintyping:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
52 --shigatoxintyping
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
53 --blastn_STX $blastn_STX
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
54 #end if
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
55 </command>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
56
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
57 <inputs>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
58 <!-- single/paired -->
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
59 <conditional name="library">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
60 <param name="type" type="select" label="Is this a single-end or paired-end library">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
61 <option value="single">Single-end</option>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
62 <option value="paired">Paired-end</option>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
63 <option value="pairedcollection">Paired-end collection</option>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
64 </param>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
65 <when value="single">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
66 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
67 </when>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
68 <when value="paired">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
69 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
70 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
71 </when>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
72 <when value="pairedcollection">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
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" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
74 </when>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
75 </conditional>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
76 <param name="serotyping" type="boolean" checked="true" label="Perform Serotyping" help="" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
77 <param name="virulotyping" type="boolean" checked="true" label="Perform Virulotyping" help="" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
78 <param name="shigatoxintyping" type="boolean" checked="true" label="Perform Shigatoxintyping" help="" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
79 </inputs>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
80
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
81 <!-- define outputs -->
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
82 <outputs>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
83 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
84 <data format="txt" name="text_file_1" label="${tool.name} on ${on_string}: RawData" hidden="true" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
85 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
86 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
87 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
88 <data format="txt" name="text_file_2" label="${tool.name} on ${on_string}: RawData reverse" hidden="true">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
89 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
90 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
91 <data name="trimmed1" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
92 #if str( $library.type ) == 'paired'#
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
93 forward
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
94 #end if#
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
95 FASTQ">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
96 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
97 <data name="trimmed2" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed reverse FASTQ">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
98 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
99 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
100 <data name="trimmedunpaired" format="fastqsanger" label="${tool.name} on ${on_string}: trimmed unpaired reads">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
101 <filter>library['type'] == 'paired' or library['type'] == 'pairedcollection'</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
102 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
103 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
104 <data name="virulotyper" format="tabular" label="Virulotyper on ${on_string}: Mapping reads" hidden="true">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
105 <filter>virulotyping</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
106 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
107 <data name="blastn_STX" format="tabular" label="Blastn for Shiga toxin on ${on_string}" hidden="true" >
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
108 <filter>shigatoxintyping</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
109 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
110 <data name="mlstsevenloci" format="tabular" label="Multi Locus on ${on_string}: Alleles Table" hidden="true" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
111 <data name="spades_log" format="txt" label="SPAdes log" hidden="true">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
112 <filter>serotyping</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
113 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
114 <data name="blastn_O" format="tabular" label="Blastn for O on ${on_string}" hidden="true">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
115 <filter>serotyping</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
116 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
117 <data name="blastn_H" format="tabular" label="Blastn for H on ${on_string}" hidden="true">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
118 <filter>serotyping</filter>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
119 </data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
120 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
121 </outputs>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
122
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
123 <tests>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
124 <test>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
125 <!-- basic test on contigs file -->
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
126 <param name="type" value="single"/>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
127 <param name="input_1" value="a_reads.fastq" ftype="fastqsanger"/>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
128 <param name="serotyping" value="true"/>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
129 <output name="report_out">
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
130 <assert_contents>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
131 <has_text text="wzx_208_AF529080_O26" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
132 <has_text text="wzy_192_AF529080_O26" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
133 <has_text text="fliC_269_AY337465_H11" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
134 <has_text text="fliC_276_AY337472_H11" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
135 </assert_contents>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
136 </output>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
137 <output name="blastn_O" file="blastn_O" ftype="tabular" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
138 <output name="blastn_H" file="blastn_H" ftype="tabular" />
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
139 </test>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
140 </tests>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
141
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
142 <help>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
143 **EURL VTEC WGS PT Overview**
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
144 This tool performs various typing tools:
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
145
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
146 - Raw data quality check (FASTQC)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
147
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
148 - Trimming (FASTQ positional and quality trimming)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
149
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
150 - Virulotyping (patho_typing tool from the INNUENDO Project)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
151
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
152 - Multi Locus Sequence Typing (MentaLiST 7 loci)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
153
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
154 - Filtering (DUK)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
155
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
156 - Assembly (SPAdes)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
157
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
158 - Serotyping (blastn)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
159
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
160 - Shigatoxintyping (blastn against the shiga toxin subtype database from the Statens Serum Institut (SSI) and Technical University of Denmark DTU)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
161
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
162 Istituto Superiore di Sanità
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
163
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
164 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
165
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
166 Developer: Arnold Knijn arnold.knijn@iss.it
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
167
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
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
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
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”
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
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)
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
171 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
172 </help>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
173 <citations>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
174 <citation type="bibtex">@ARTICLE{andrews_s,
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
175 author = {Andrews, S},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
176 keywords = {bioinformatics, ngs, qc},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
177 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
178 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
179 }</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
180 <citation type="doi">10.1093/bioinformatics/btu135</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
181 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
182 <citation type="doi">10.1038/nmeth.1923</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
183 <citation type="doi">10.1099/mgen.0.000146</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
184 <citation type="bibtex">@ARTICLE{li-copeland,
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
185 author = {Li, M, Copeland, A, and Han, J},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
186 keywords = {bioinformatics, ngs},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
187 title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
188 url = {https://www.osti.gov/servlets/purl/1016000/}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
189 }</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
190 <citation type="bibtex">@ARTICLE{edwards_ra,
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
191 author = {Edwards, RA},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
192 keywords = {bioinformatics, ngs},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
193 title = {{fastq-pair}},
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
194 url = {https://github.com/linsalrob/EdwardsLab/}
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
195 }</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
196 <citation type="doi">10.1089/cmb.2012.0021</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
197 <citation type="doi">10.1186/1471-2105-10-421</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
198 <citation type="doi">10.1186/s13742-015-0080-7</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
199 <citation type="doi">10.1128/JCM.00008-15</citation>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
200 </citations>
965517909457 planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
cstrittmatter
parents:
diff changeset
201 </tool>