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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Mon, 20 Jan 2020 10:50:35 -0500
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1 <tool id="ecoliserotyper" name="E coli Serotyper" version="1.2">
2 <description>performs serotyping of Escherichia coli
3 </description>
4 <requirements>
5 <requirement type="package" version="3.7">python</requirement>
6 <requirement type="package" version="1.4">scipy</requirement>
7 <requirement type="package" version="5.26">perl</requirement>
8 <requirement type="package" version="1.7.2">perl-bioperl</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="0.7.8">bwa</requirement>
13 <requirement type="package" version="2.7.1">blast</requirement>
14 <requirement type="package" version="3.12.0">spades</requirement>
15 <requirement type="package" version="0.11.8">fastqc</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__/Ecoli_Serotyper.py --input_type ${origin.input_type} --log $logfile --output $report_out --blastn_O $blastn_O --blastn_H $blastn_H
24 #if str( $origin.input_type ) == "contigs":
25 -1 $origin.input_1 --input1_name '$origin.input_1.name'
26 #else:
27 -1 $origin.library.input_1 --input1_ext ${origin.library.input_1.ext} --input1_name '${origin.library.input_1.name}'
28 --html1 $html_file_1 --html1_id $__app__.security.encode_id($html_file_1.dataset.id) --html1_path ${html_file_1.files_path}
29 --spades_log $spades_log
30 #if str( $origin.library.type ) == "paired":
31 -2 $origin.library.input_2 --input2_ext ${origin.library.input_2.ext} --input2_name '${origin.library.input_2.name}'
32 --html2 $html_file_2 --html2_id $__app__.security.encode_id($html_file_2.dataset.id) --html2_path ${html_file_2.files_path}
33 #end if
34 #end if
35 </command>
36
37 <inputs>
38 <!-- fastq/contigs -->
39 <conditional name="origin">
40 <param name="input_type" type="select" label="Are the input files FASTQ or Contigs">
41 <option value="fastq">FASTQ</option>
42 <option value="contigs">Contigs</option>
43 </param>
44
45 <when value="fastq">
46 <!-- single/paired -->
47 <conditional name="library">
48 <param name="type" type="select" label="Is this single or paired library">
49 <option value="single">Single-end</option>
50 <option value="paired">Paired-end</option>
51 </param>
52
53 <when value="single">
54 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file" help="Must be of datatype &quot;fastqsanger&quot;" />
55 </when>
56 <when value="paired">
57 <param name="input_1" format="fastqsanger" type="data" label="FASTQ file #1" help="Must be of datatype &quot;fastqsanger&quot;" />
58 <param name="input_2" format="fastqsanger" type="data" label="FASTQ file #2" help="Must be of datatype &quot;fastqsanger&quot;" />
59 </when>
60 </conditional>
61 </when>
62 <when value="contigs">
63 <param name="input_1" format="fasta" type="data" label="FASTA Contigs file" help="Must be of datatype &quot;fasta&quot;" />
64 </when>
65 </conditional>
66 </inputs>
67
68 <!-- define outputs -->
69 <outputs>
70 <data format="html" name="html_file_1" label="${tool.name} on ${on_string}: Webpage" hidden="true">
71 <filter>origin['input_type'] == 'fastq'</filter>
72 </data>
73 <data format="html" name="html_file_2" label="${tool.name} on ${on_string}: Webpage reverse" hidden="true">
74 <filter>origin['input_type'] == 'fastq' and origin['library']['type'] == 'paired'</filter>
75 </data>
76 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" />
77 <data name="spades_log" format="txt" label="SPAdes log" hidden="true">
78 <filter>origin['input_type'] == 'fastq'</filter>
79 </data>
80 <data name="blastn_O" format="tabular" label="Blastn for O" hidden="true" />
81 <data name="blastn_H" format="tabular" label="Blastn for H" hidden="true" />
82 <data name="report_out" format="html" label="${tool.name} on ${on_string}: report"></data>
83 </outputs>
84
85 <tests>
86 <test>
87 <!-- basic test on contigs file -->
88 <param name="input_type" value="contigs"/>
89 <param name="input_1" value="a_contigs.fasta" ftype="fasta"/>
90 <param name="input1_name" value="a_contigs.fasta"/>
91 <output name="report_out">
92 <assert_contents>
93 <has_text text="wzx_208_AF529080_O26" />
94 <has_text text="wzy_192_AF529080_O26" />
95 <has_text text="fliC_269_AY337465_H11" />
96 <has_text text="fliC_276_AY337472_H11" />
97 </assert_contents>
98 </output>
99 <output name="blastn_O" file="blastn_O" ftype="tabular" />
100 <output name="blastn_H" file="blastn_H" ftype="tabular" />
101 </test>
102 </tests>
103
104 <help>
105 **E coli Serotyper Overview**
106
107 This tool performs various operations:
108
109 - Optionally: Quality assessment (FastQC)
110
111 - Optionally: Trimming (FASTQ positional and quality trimming)
112
113 - Optionally: Filtering (DUK)
114
115 - Optionally: Assembly (SPAdes)
116
117 - Serotyping (Blast+ against serotype databases from the Center for Genomic Epidemiology CGE)
118
119 Istituto Superiore di Sanita'
120
121 European Union Reference Laboratory (EU-RL) for Escherichia coli, including Verotoxigenic E. coli (VTEC)
122
123 Developer: Arnold Knijn arnold.knijn@iss.it
124
125 </help>
126 <citations>
127 <citation type="bibtex">@ARTICLE{andrews_s,
128 author = {Andrews, S},
129 keywords = {bioinformatics, ngs, qc},
130 priority = {2},
131 title = {{FastQC A Quality Control tool for High Throughput Sequence Data}},
132 url = {http://www.bioinformatics.babraham.ac.uk/projects/fastqc/}
133 }</citation>
134 <citation type="bibtex">@ARTICLE{andrews_s,
135 author = {Li, M, Copeland, A, and Han, J},
136 keywords = {bioinformatics, ngs},
137 title = {{DUK – A Fast and Efficient Kmer Based Sequence Matching Tool}},
138 url = {https://www.osti.gov/servlets/purl/1016000/}
139 }</citation>
140 <citation type="bibtex">@ARTICLE{andrews_s,
141 author = {Edwards, RA},
142 keywords = {bioinformatics, ngs},
143 title = {{fastq-pair}},
144 url = {https://github.com/linsalrob/EdwardsLab/}
145 }</citation>
146 <citation type="doi">10.1089/cmb.2012.0021</citation>
147 <citation type="doi">10.1186/1471-2105-10-421</citation>
148 <citation type="doi">10.1186/s13742-015-0080-7</citation>
149 <citation type="doi">10.1128/JCM.00008-15</citation>
150 </citations>
151 </tool>