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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/seqsero2 commit 8b41cf1161ac0f0836f5597167911596b0cfa27e-dirty"
author thanhlv
date Fri, 12 Nov 2021 14:56:56 +0000
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1 <tool id="seqsero2" name="SeqSero2" version="@VERSION@+galaxy0">
2 <description> Salmonella serotype prediction</description>
3 <macros>
4 <token name="@VERSION@">1.2.1</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">seqsero2</requirement>
8 </requirements>
9 <version_command>SeqSero2_package.py -v</version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 #import re
12 #set $seqsero_input = ''
13 #set $seqsero_t_value = ''
14 #if $inputs.input_type == 'paired':
15 #if $inputs.R1.is_of_type('fastqsanger', 'fastq'):
16 #set $ext = 'fastq'
17 #elif $inputs.R1.is_of_type('fastqsanger.gz'):
18 #set $ext = 'fastq.gz'
19 #elif $inputs.R1.is_of_type('fastq'):
20 #set $ext = 'fastq'
21 #elif $inputs.R1.is_of_type('fastq.gz'):
22 #set $ext = 'fastq.gz'
23 #elif $inputs.R1.is_of_type('fasta.gz'):
24 #set $ext = 'fasta.gz'
25 #elif $inputs.R1.is_of_type('fasta'):
26 #set $ext = 'fasta'
27 #end if
28 #set $safename_R1 = re.sub('[^\w\-_\.]', '_', $inputs.R1.element_identifier)
29 #set $safename_R2 = re.sub('[^\w\-_\.]', '_', $inputs.R2.element_identifier)
30 ln -fs '$inputs.R1' $safename_R1.$ext &&
31 ln -fs '$inputs.R2' $safename_R2.$ext &&
32 #set $seqsero_input = $safename_R1 + '.' + $ext + ' ' + $safename_R2 + '.' + $ext
33 #set $seqsero_t_value = '2'
34 #elif $inputs.input_type == 'collection':
35 #for $input in $inputs.input_collection
36 #if $input.forward.is_of_type('fastqsanger', 'fastq'):
37 #set $ext = 'fastq'
38 #elif $input.forward.is_of_type('fastqsanger.gz'):
39 #set $ext = 'fastq.gz'
40 #elif $input.forward.is_of_type('fastq'):
41 #set $ext = 'fastq'
42 #elif $input.forward.is_of_type('fastq.gz'):
43 #set $ext = 'fastq.gz'
44 #elif $input.forward.is_of_type('fasta.gz'):
45 #set $ext = 'fasta.gz'
46 #elif $input.forward.is_of_type('fasta'):
47 #set $ext = 'fasta'
48 #end if
49 #set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.forward.element_identifier)
50 ln -fs '$input.forward' $safename_fwd.$ext &&
51 #set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.reverse.element_identifier)
52 ln -fs '$input.reverse' $safename_rvs.$ext &&
53 #set $seqsero_input = $safename_fwd+ '.' + $ext + ' ' + $safename_rvs + '.' + $ext
54 #set $seqsero_t_value = '2'
55 #end for
56 #elif $inputs.input_type == 'assembly':
57 #if $inputs.contigs.is_of_type('fasta.gz'):
58 #set $ext = 'fasta.gz'
59 #elif $inputs.contigs.is_of_type('fasta'):
60 #set $ext = 'fasta'
61 #end if
62 #set $safename_seq = re.sub('[^\w\-_\.]', '_', $contigs.element_identifier)
63 ln -fs '$contigs' $safename_seq.$ext &&
64 #set $seqsero_input = $safename_seq + '.' + $ext
65 #set $seqsero_t_value = '4'
66 #elif $inputs.input_type == 'single':
67 #if $inputs.single.is_of_type('fastqsanger', 'fastq'):
68 #set $ext = 'fastq'
69 #elif $inputs.single.is_of_type('fastqsanger.gz'):
70 #set $ext = 'fastq.gz'
71 #elif $inputs.single.is_of_type('fastq'):
72 #set $ext = 'fastq'
73 #elif $inputs.single.is_of_type('fastq.gz'):
74 #set $ext = 'fastq.gz'
75 #elif $inputs.single.is_of_type('fasta.gz'):
76 #set $ext = 'fasta.gz'
77 #elif $inputs.single.is_of_type('fasta'):
78 #set $ext = 'fasta'
79 #end if
80 #set $safename_seq = re.sub('[^\w\-_\.]', '_', $single.element_identifier)
81 ln -fs '$single' $safename_seq.$ext &&
82 #set $seqsero_input = $safename_seq + '.' + $ext
83 #set $seqsero_t_value = '3'
84 #elif $inputs.input_type == 'nanopore':
85 #if $inputs.nanopore.is_of_type('fastqsanger', 'fastq'):
86 #set $ext = 'fastq'
87 #elif $inputs.nanopore.is_of_type('fastqsanger.gz'):
88 #set $ext = 'fastq.gz'
89 #elif $inputs.nanopore.is_of_type('fastq'):
90 #set $ext = 'fastq'
91 #elif $inputs.nanopore.is_of_type('fastq.gz'):
92 #set $ext = 'fastq.gz'
93 #elif $inputs.nanopore.is_of_type('fasta.gz'):
94 #set $ext = 'fasta.gz'
95 #elif $inputs.nanopore.is_of_type('fasta'):
96 #set $ext = 'fasta'
97 #end if
98 #set $safename_seq = re.sub('[^\w\-_\.]', '_', $nanopore.element_identifier)
99 ln -fs '$nanopore' $safename_seq.$ext &&
100 #set $seqsero_input = $safename_seq + '.' + $ext
101 #set $seqsero_t_value = '5'
102 #end if
103
104 SeqSero2_package.py
105 -m $workflow
106 -t $seqsero_t_value
107 -i $seqsero_input
108 -p \${GALAXY_SLOTS:-4}
109 -d output
110 ]]> </command>
111 <inputs>
112 <conditional name="inputs">
113 <param name="input_type" type="select" label="Input type" help="Select 'paired end' reads or 'sequence' for genomes/contigs">
114 <option value="paired">Paired End</option>
115 <option value="collection">Collection</option>
116 <option value="assembly">Contigs</option>
117 <option value="single">Interleaved</option>
118 <option value="nanopore">Nanopore reads</option>
119 </param>
120 <when value="paired">
121 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
122 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
123 </when>
124 <when value="collection">
125 <param name="input_collection" format="fastqsanger" type="data_collection" collection_type="list:paired" label="Paired collection"/>
126 </when>
127 <when value="single">
128 <param name="single" type="data" format="fastqsanger,fastqsanger.gz" multiple="false" label="Interleaved" />
129 </when>
130 <when value="nanopore">
131 <param name="nanopore" type="data" format="fastqsanger,fastqsanger.gz" multiple="false" label="Nanopore reads" />
132 </when>
133 <when value="assembly">
134 <param name="contigs" type="data" format="fasta" multiple="false" label="Contigs/genomes" />
135 </when>
136 </conditional>
137 <param label="Workflow" type="select" name="workflow">
138 <option value="a">allele</option>
139 <option value="k" selected="true">k-mer</option>
140 </param>
141 </inputs>
142 <outputs>
143 <data name="results" format="tabular" label="${tool.name} on ${on_string} Results" from_work_dir="output/SeqSero_result.tsv"/>
144 <data name="log" format="txt" label="${tool.name} on ${on_string} Log" from_work_dir="output/SeqSero_log.txt"/>
145
146 </outputs>
147 <tests>
148 <test>
149 <param name="input_type" value="assembly" />
150 <param name="contigs" value="CP009102.1.fasta" ftype="fasta" />
151 <output name="results">
152 <assert_contents>
153 <has_text text="Salmonella enterica subspecies enterica (subspecies I)" />
154 <has_text text="Typhimurium" />
155 </assert_contents>
156 </output>
157 </test>
158 <!-- TODO: Test for fastq files -->
159 </tests>
160 <help><![CDATA[
161
162 **Usage: SeqSero2_package.py**
163
164 -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a)
165
166 -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore reads (fasta/fastq))
167
168 -i <file> (/path/to/input/file)
169
170 -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1)
171
172 -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode)
173
174 -d <string> (output directory name)
175
176 -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files)
177
178 -n <string> (optional, to specify a sample name in the report output)
179
180 -s <flag> (if '-s' was flagged, SeqSero2 will not output header in `SeqSero_result.tsv`)
181
182 --check <flag> (use '--check' flag to check the required dependencies)
183
184 -v, --version (show program's version number and exit)
185
186 -----
187
188 _`Document`: https://github.com/denglab/SeqSero2
189
190 ]]></help>
191 <citations>
192 <citation type="bibtex">
193 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015, title={Salmonella serotype determination utilizing high-throughput genome sequencing data.}, journal={J Clin Microbiol}, publisher={ASM}, author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.}, year={2015}, month={Max}, url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
194 }</citation>
195 <citation type="bibtex">
196 @misc{cfsan_biostatistics_group_2017, title={CFSAN Biostatistics Group fork of SeqSero2}, url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
197 </citation>
198 </citations>
199
200 </tool>