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author jpayne
date Mon, 29 Sep 2025 20:04:28 +0000
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1 <tool id="seqsero2s" name="SeqSero2S" version="1">
2 <description>Simplified Salmonella serotype prediction</description>
3 <requirements>
4 <!-- <requirement type="package" version="@VERSION@">seqsero2s</requirement> -->
5 <container type="docker">quay.io/biocontainers/seqsero2s:1.1.3--pyhdfd78af_0</container>
6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[
8 mkdir ./output;
9
10 #if $reads.reads_select == 'history'
11 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
12 #set $forward = $reads.forward
13 #set $reverse = $reads.reverse
14 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
15 #set $tval = 2
16 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
17 gunzip -c $reverse > reverse.fastq;
18 #set $reverse = './reverse.fastq'
19 gunzip -c $forward > forward.fastq;
20 #set $forward = './forward.fastq'
21 #end if
22 ln -s $forward ${name}_1.fastq;
23 ln -s $reverse ${name}_2.fastq;
24 #else if $reads.reads_select == 'collection'
25 #set $name = $reads.coll.name.replace(' ', '_')
26 #set $forward = $reads.coll.forward
27 #set $reverse = $reads.coll.reverse
28 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
29 #set $tval = 2
30 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
31 gunzip -c $reverse > reverse.fastq;
32 #set $reverse = './reverse.fastq'
33 gunzip -c $forward > forward.fastq;
34 #set $forward = './forward.fastq'
35 #end if
36 ln -s $forward ${name}_1.fastq;
37 ln -s $reverse ${name}_2.fastq;
38 #else
39 #set $name = $reads.assembly.name.replace(' ', '_')
40 #set $ga = $reads.assembly
41 #set $infile = $name + ".fasta"
42 ln -s $ga ${name}.fasta;
43 #set $tval = 4
44 #set $mode='k'
45 #end if
46 echo $name ;
47 echo "-=-=-=-=-" ;
48 touch output/SeqSero_log.txt ;
49 /usr/local/bin/SeqSero2S.py --version ;
50 echo "-=-=-=-=-" ;
51 /usr/local/bin/SeqSero2S.py
52 -p \${GALAXY_SLOTS:-1}
53 -t $tval
54 -m $mode
55 -d ./output
56 #if $mode == 'a':
57 -b $maptype
58 #end if
59 -i $infile &&
60 echo "-=-=-=-=-" &&
61 cat output/SeqSero_log.txt &&
62 echo "-=-=-=-=-" &&
63 ls -lah ./output
64 ]]></command>
65 <inputs>
66
67 <conditional name="reads">
68 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
69 <option value="collection">Paired collection from your history</option>
70 <option value="history">Two FASTQ datasets from your history</option>
71 <option value="genome">Genome Assembly</option>
72 </param>
73 <when value="collection">
74 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
75 </when>
76 <when value="history">
77 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
78 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
79 </when>
80 <when value="genome">
81 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
82 </when>
83 </conditional>
84
85 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
86 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
87 <!-- <param name="numofthr" type="select" label="Number of threads">
88 <option value="1">1</option>
89 <option value="2">2</option>
90 <option value="3">3</option>
91 <option value="4">4</option> -->
92 <!-- </param> -->
93
94 <param label="Analysis mode" type="select" name="mode">
95 <option value="a">allele mode</option>
96 <option value="k">k-mer mode</option>
97 </param>
98
99 <param name="maptype" type="select" label="Algorithms for BWA mapping">
100 <option value="mem">mem</option>
101 <option value="sam">sam</option>
102 </param>
103
104
105
106 </inputs>
107 <outputs>
108 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv" />
109 </outputs>
110 <tests>
111 <!-- <test>
112 <param name="reads_select" value="history" />
113 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
114 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
115 <output name="results" file="Seqsero_result.tsv" />
116 </test>
117 <test>
118 <param name="reads_select" value="collection" />
119 <param name="coll">
120 <collection type="paired">
121 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
122 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
123 </collection>
124 </param>
125 <output name="results" file="Seqsero_result.tsv" />
126 </test> -->
127 <!-- <test>
128 <param name="mode" value="k" />
129 <param name="reads_select" value="history" />
130 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
131 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
132 <output name="results" file="Seqsero_result_25k.tsv" />
133 </test>
134 <test>
135 <param name="mode" value="k" />
136 <param name="reads_select" value="collection" />
137 <param name="coll">
138 <collection type="paired">
139 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
140 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
141 </collection>
142 </param>
143 <output name="results" file="Seqsero_result_25k_coll.tsv" />
144 </test>
145 <test>
146 <param name="mode" value="a" />
147 <param name="reads_select" value="history" />
148 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
149 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
150 <assert_stdout>
151 <has_text text="input genome cannot be identified as Salmonella" />
152 </assert_stdout>
153 </test> -->
154 <!-- <test>
155 <param name="mode" value="a" />
156 <param name="reads_select" value="collection" />
157 <param name="coll">
158 <collection type="paired">
159 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
160 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
161 </collection>
162 </param>
163 <output name="results" file="Seqsero_result_allele.tsv" />
164 </test> -->
165 <test>
166 <param name="mode" value="k" />
167 <param name="reads_select" value="genome" />
168 <param name="assembly" value="test/taxonomy/salmonella/contigs.fa" ftype="fasta" />
169 <output name="results" file="test/taxonomy/salmonella/SeqSero_result/SeqSero_result.tsv" />
170 </test>
171 </tests>
172 <help><![CDATA[
173
174 **Usage: SeqSero2.py**
175
176 **Algorithms for BWA mapping**
177
178 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
179
180 ]]></help>
181 <citations>
182 <citation type="bibtex">
183 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
184 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
185 journal={J Clin Microbiol}, publisher={ASM},
186 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
187 year={2015}, month={Max},
188 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
189 }</citation>
190 <citation type="bibtex">
191 @misc{cfsan_biostatistics_group_2017,
192 title={CFSAN Biostatistics Group fork of SeqSero2},
193 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
194 </citation>
195 </citations>
196
197 </tool>