Mercurial > repos > jpayne > seqsero_v2

comparison seqsero.xml @ 15:1d6702e0bffd

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Wed, 01 Mar 2023 13:20:59 -0500
parents
children
comparison
equal deleted inserted replaced
14:496f5f2b5e75 15:1d6702e0bffd
1 <tool id="seqsero_v2" name="SeqSero2 v1.2.1" version="8">
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 <command detect_errors="exit_code"><![CDATA[
10 echo "SeqSero2 v1.2.1";
11 mkdir ./output;
12
13 #if $reads.reads_select == 'history'
14 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
15 #set $forward = $reads.forward
16 #set $reverse = $reads.reverse
17 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
18 #set $tval = 2
19 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
20 gunzip -c $reverse > reverse.fastq;
21 #set $reverse = './reverse.fastq'
22 gunzip -c $forward > forward.fastq;
23 #set $forward = './forward.fastq'
24 #end if
25 ln -s $forward ${name}_1.fastq;
26 ln -s $reverse ${name}_2.fastq;
27 #else if $reads.reads_select == 'collection'
28 #set $name = $reads.coll.name.replace(' ', '_')
29 #set $forward = $reads.coll.forward
30 #set $reverse = $reads.coll.reverse
31 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
32 #set $tval = 2
33 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
34 gunzip -c $reverse > reverse.fastq;
35 #set $reverse = './reverse.fastq'
36 gunzip -c $forward > forward.fastq;
37 #set $forward = './forward.fastq'
38 #end if
39 ln -s $forward ${name}_1.fastq;
40 ln -s $reverse ${name}_2.fastq;
41 #else
42 #set $name = $reads.assembly.name.replace(' ', '_')
43 #set $ga = $reads.assembly
44 #set $infile = $name + ".fasta"
45 ln -s $ga ${name}.fasta;
46 #set $tval = 4
47 #set $mode='k'
48 #end if
49 echo $name ;
50 echo "-=-=-=-=-" ;
51 touch output/SeqSero_log.txt ;
52 SeqSero2_package.py
53 -p \${GALAXY_SLOTS:-1}
54 -t $tval
55 -m $mode
56 -d ./output
57 #if $mode == 'a':
58 -b $maptype
59 #end if
60 -i $infile &&
61 echo "-=-=-=-=-" &&
62 cat output/SeqSero_log.txt &&
63 echo "-=-=-=-=-" &&
64 ls -lah ./output
65 ]]></command>
66 <inputs>
67
68 <conditional name="reads">
69 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
70 <option value="collection">Paired collection from your history</option>
71 <option value="history">Two FASTQ datasets from your history</option>
72 <option value="genome">Genome Assembly</option>
73 </param>
74 <when value="collection">
75 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
76 </when>
77 <when value="history">
78 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
79 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
80 </when>
81 <when value="genome">
82 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
83 </when>
84 </conditional>
85
86 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
87 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
88 <!-- <param name="numofthr" type="select" label="Number of threads">
89 <option value="1">1</option>
90 <option value="2">2</option>
91 <option value="3">3</option>
92 <option value="4">4</option> -->
93 <!-- </param> -->
94
95 <param label="Analysis mode" type="select" name="mode">
96 <option value="a">allele mode</option>
97 <option value="k">k-mer mode</option>
98 </param>
99
100 <param name="maptype" type="select" label="Algorithms for BWA mapping">
101 <option value="mem">mem</option>
102 <option value="sam">sam</option>
103 </param>
104
105
106
107 </inputs>
108 <outputs>
109 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/>
110 </outputs>
111 <tests>
112 <!-- <test>
113 <param name="reads_select" value="history" />
114 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
115 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
116 <output name="results" file="Seqsero_result.tsv" />
117 </test>
118 <test>
119 <param name="reads_select" value="collection" />
120 <param name="coll">
121 <collection type="paired">
122 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
123 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
124 </collection>
125 </param>
126 <output name="results" file="Seqsero_result.tsv" />
127 </test> -->
128 <test>
129 <param name="mode" value="k" />
130 <param name="reads_select" value="history" />
131 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
132 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
133 <output name="results" file="Seqsero_result_25k.tsv" />
134 </test>
135 <test>
136 <param name="mode" value="k" />
137 <param name="reads_select" value="collection" />
138 <param name="coll">
139 <collection type="paired">
140 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
141 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
142 </collection>
143 </param>
144 <output name="results" file="Seqsero_result_25k_coll.tsv" />
145 </test>
146 <test>
147 <param name="mode" value="a" />
148 <param name="reads_select" value="history" />
149 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
150 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
151 <assert_stdout>
152 <has_text text="predicted antigenic profile does not exist" />
153 </assert_stdout>
154 </test>
155 <!-- <test>
156 <param name="mode" value="a" />
157 <param name="reads_select" value="collection" />
158 <param name="coll">
159 <collection type="paired">
160 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
161 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
162 </collection>
163 </param>
164 <output name="results" file="Seqsero_result_allele.tsv" />
165 </test> -->
166 </tests>
167 <help><![CDATA[
168
169 **Usage: SeqSero2.py**
170
171 **Algorithms for BWA mapping**
172
173 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
174
175 ]]></help>
176 <citations>
177 <citation type="bibtex">
178 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
179 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
180 journal={J Clin Microbiol}, publisher={ASM},
181 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
182 year={2015}, month={Max},
183 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
184 }</citation>
185 <citation type="bibtex">
186 @misc{cfsan_biostatistics_group_2017,
187 title={CFSAN Biostatistics Group fork of SeqSero2},
188 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
189 </citation>
190 </citations>
191
192 </tool>