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comparison seqsero2.xml @ 8:7dd264cd634e

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author estrain
date Fri, 06 Sep 2019 22:31:30 -0400
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1 <tool id="seqsero2_v1_0_1" name="SeqSero 2" version="1.0.1">
2 <description>Salmonella serotype prediction</description>
3 <requirements>
4 <requirement type="package" version="3.6">python</requirement>
5 <requirement type="package" version="1.73">biopython</requirement>
6 <requirement type="package" version="2.7.1">blast</requirement>
7 <requirement type="package" version="1.9">samtools</requirement>
8 <requirement type="package" version="2.9.1">sra-tools</requirement>
9 <requirement type="package" version="0.7.17">bwa</requirement>
10 <requirement type="package" version="3.13.1">spades</requirement>
11 <requirement type="package" version="2.27.1">bedtools</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[
14 echo "SeqSero 2 v. 1.0.1" ;
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 #else
20 #set $name = $reads.coll.name.replace(' ', '_')
21 #set $forward = $reads.coll.forward
22 #set $reverse = $reads.coll.reverse
23 #end if
24 echo $name ;
25 echo "-=-=-=-=-" ;
26 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
27 gunzip -c $forward > forward.fastq;
28 #set $forward = './forward.fastq'
29 #end if
30 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
31 gunzip -c $reverse > reverse.fastq;
32 #set $reverse = './reverse.fastq'
33 #end if
34 ln -s $forward ${name}_1.fastq;
35 ln -s $reverse ${name}_2.fastq;
36 mkdir ./output;
37 touch output/SeqSero_log.txt ;
38 python $__tool_directory__/SeqSero2_package.py
39 -p \${GALAXY_SLOTS:-4}
40 -t 2
41 -m $mode
42 -d ./output
43 #if $mode == 'a':
44 -b $maptype
45 #end if
46 -i ${name}_1.fastq ${name}_2.fastq &&
47 echo "-=-=-=-=-" &&
48 cat output/SeqSero_log.txt &&
49 echo "-=-=-=-=-" &&
50 ls -lah ./output
51 ]]></command>
52 <inputs>
53
54 <conditional name="reads">
55 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
56 <option value="collection">Paired collection from your history</option>
57 <option value="history">Two FASTQ datasets from your history</option>
58 </param>
59 <when value="collection">
60 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
61 </when>
62 <when value="history">
63 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
64 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
65 </when>
66 </conditional>
67
68 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
69 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
70 <!-- <param name="numofthr" type="select" label="Number of threads">
71 <option value="1">1</option>
72 <option value="2">2</option>
73 <option value="3">3</option>
74 <option value="4">4</option> -->
75 <!-- </param> -->
76
77 <param label="Analysis mode" type="select" name="mode">
78 <option value="a">allele mode</option>
79 <option value="k">k-mer mode</option>
80 </param>
81
82 <param name="maptype" type="select" label="Algorithms for BWA mapping">
83 <option value="mem">mem</option>
84 <option value="sam">sam</option>
85 </param>
86
87
88
89 </inputs>
90 <outputs>
91 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
92 </outputs>
93 <tests>
94 <!-- <test>
95 <param name="reads_select" value="history" />
96 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
97 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
98 <output name="results" file="Seqsero_result.tsv" />
99 </test>
100 <test>
101 <param name="reads_select" value="collection" />
102 <param name="coll">
103 <collection type="paired">
104 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
105 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
106 </collection>
107 </param>
108 <output name="results" file="Seqsero_result.tsv" />
109 </test> -->
110 <test>
111 <param name="mode" value="k" />
112 <param name="reads_select" value="history" />
113 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
114 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
115 <output name="results" file="Seqsero_result_25k.tsv" />
116 </test>
117 <test>
118 <param name="mode" value="k" />
119 <param name="reads_select" value="collection" />
120 <param name="coll">
121 <collection type="paired">
122 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
123 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
124 </collection>
125 </param>
126 <output name="results" file="Seqsero_result_25k_coll.tsv" />
127 </test>
128 <test>
129 <param name="mode" value="a" />
130 <param name="reads_select" value="history" />
131 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
132 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
133 <assert_stdout>
134 <has_text text="predicted antigenic profile does not exist" />
135 </assert_stdout>
136 </test>
137 <!-- <test>
138 <param name="mode" value="a" />
139 <param name="reads_select" value="collection" />
140 <param name="coll">
141 <collection type="paired">
142 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
143 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
144 </collection>
145 </param>
146 <output name="results" file="Seqsero_result_allele.tsv" />
147 </test> -->
148 </tests>
149 <help><![CDATA[
150
151 **Usage: SeqSero2.py**
152
153 **Algorithms for BWA mapping**
154
155 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
156
157 ]]></help>
158 <citations>
159 <citation type="bibtex">
160 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
161 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
162 journal={J Clin Microbiol}, publisher={ASM},
163 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
164 year={2015}, month={Max},
165 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
166 }</citation>
167 <citation type="bibtex">
168 @misc{cfsan_biostatistics_group_2017,
169 title={CFSAN Biostatistics Group fork of SeqSero2},
170 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
171 </citation>
172 </citations>
173
174 </tool>