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planemo upload commit 233f498f942f9253a7e6e1656157e59d38549c44-dirty
author jpayne
date Fri, 15 Aug 2025 19:51:19 +0000
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1 <tool id="seqsero_v2" name="SeqSero2 v1.3.1" version="9">
2 <description>Salmonella serotype prediction</description>
3 <macros>
4 <token name="@VERSION@">1.3.1</token>
5 </macros>
6 <requirements>
7 <!-- <requirement type="package" version="@VERSION@">seqsero2</requirement> -->
8 <container>
9 <image>seqsero2:1.3.1</image>
10 </container>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13 mkdir ./output;
14
15 #if $reads.reads_select == 'history'
16 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
17 #set $forward = $reads.forward
18 #set $reverse = $reads.reverse
19 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
20 #set $tval = 2
21 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
22 gunzip -c $reverse > reverse.fastq;
23 #set $reverse = './reverse.fastq'
24 gunzip -c $forward > forward.fastq;
25 #set $forward = './forward.fastq'
26 #end if
27 ln -s $forward ${name}_1.fastq;
28 ln -s $reverse ${name}_2.fastq;
29 #else if $reads.reads_select == 'collection'
30 #set $name = $reads.coll.name.replace(' ', '_')
31 #set $forward = $reads.coll.forward
32 #set $reverse = $reads.coll.reverse
33 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
34 #set $tval = 2
35 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
36 gunzip -c $reverse > reverse.fastq;
37 #set $reverse = './reverse.fastq'
38 gunzip -c $forward > forward.fastq;
39 #set $forward = './forward.fastq'
40 #end if
41 ln -s $forward ${name}_1.fastq;
42 ln -s $reverse ${name}_2.fastq;
43 #else
44 #set $name = $reads.assembly.name.replace(' ', '_')
45 #set $ga = $reads.assembly
46 #set $infile = $name + ".fasta"
47 ln -s $ga ${name}.fasta;
48 #set $tval = 4
49 #set $mode='k'
50 #end if
51 echo $name ;
52 echo "-=-=-=-=-" ;
53 touch output/SeqSero_log.txt ;
54 SeqSero2_package.py --version ;
55 echo "-=-=-=-=-" ;
56 SeqSero2_package.py
57 -p \${GALAXY_SLOTS:-1}
58 -t $tval
59 -m $mode
60 -d ./output
61 #if $mode == 'a':
62 -b $maptype
63 #end if
64 -i $infile &&
65 echo "-=-=-=-=-" &&
66 cat output/SeqSero_log.txt &&
67 echo "-=-=-=-=-" &&
68 ls -lah ./output
69 ]]></command>
70 <inputs>
71
72 <conditional name="reads">
73 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
74 <option value="collection">Paired collection from your history</option>
75 <option value="history">Two FASTQ datasets from your history</option>
76 <option value="genome">Genome Assembly</option>
77 </param>
78 <when value="collection">
79 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
80 </when>
81 <when value="history">
82 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
83 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
84 </when>
85 <when value="genome">
86 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
87 </when>
88 </conditional>
89
90 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
91 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
92 <!-- <param name="numofthr" type="select" label="Number of threads">
93 <option value="1">1</option>
94 <option value="2">2</option>
95 <option value="3">3</option>
96 <option value="4">4</option> -->
97 <!-- </param> -->
98
99 <param label="Analysis mode" type="select" name="mode">
100 <option value="a">allele mode</option>
101 <option value="k">k-mer mode</option>
102 </param>
103
104 <param name="maptype" type="select" label="Algorithms for BWA mapping">
105 <option value="mem">mem</option>
106 <option value="sam">sam</option>
107 </param>
108
109
110
111 </inputs>
112 <outputs>
113 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv" />
114 </outputs>
115 <tests>
116 <!-- <test>
117 <param name="reads_select" value="history" />
118 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
119 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
120 <output name="results" file="Seqsero_result.tsv" />
121 </test>
122 <test>
123 <param name="reads_select" value="collection" />
124 <param name="coll">
125 <collection type="paired">
126 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
127 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
128 </collection>
129 </param>
130 <output name="results" file="Seqsero_result.tsv" />
131 </test> -->
132 <!-- <test>
133 <param name="mode" value="k" />
134 <param name="reads_select" value="history" />
135 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
136 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
137 <output name="results" file="Seqsero_result_25k.tsv" />
138 </test> -->
139 <!-- <test>
140 <param name="mode" value="k" />
141 <param name="reads_select" value="collection" />
142 <param name="coll">
143 <collection type="paired">
144 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
145 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
146 </collection>
147 </param>
148 <output name="results" file="Seqsero_result_25k_coll.tsv" />
149 </test> -->
150 <!-- <test>
151 <param name="mode" value="a" />
152 <param name="reads_select" value="history" />
153 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
154 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
155 <assert_stdout>
156 <has_text text="input genome cannot be identified as Salmonella" />
157 </assert_stdout>
158 </test> -->
159 <!-- <test>
160 <param name="mode" value="a" />
161 <param name="reads_select" value="collection" />
162 <param name="coll">
163 <collection type="paired">
164 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
165 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
166 </collection>
167 </param>
168 <output name="results" file="Seqsero_result_allele.tsv" />
169 </test> -->
170 <test>
171 <param name="mode" value="a" />
172 <param name="maptype" value="mem" />
173 <param name="reads_select" value="genome" />
174 <param name="assembly" value="test/taxonomy/salmonella/contigs.fa" ftype="fasta" />
175 <output name="results" file="test/taxonomy/salmonella/SeqSero_result/Seqsero_result.tsv" />
176 </test>
177 </tests>
178 <help><![CDATA[
179
180 **Usage: SeqSero2.py**
181
182 **Algorithms for BWA mapping**
183
184 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
185
186 ]]></help>
187 <citations>
188 <citation type="bibtex">
189 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
190 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
191 journal={J Clin Microbiol}, publisher={ASM},
192 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
193 year={2015}, month={Max},
194 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
195 }</citation>
196 <citation type="bibtex">
197 @misc{cfsan_biostatistics_group_2017,
198 title={CFSAN Biostatistics Group fork of SeqSero2},
199 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
200 </citation>
201 </citations>
202
203 </tool>