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planemo upload commit 9b152b4a900a8cd70df992da881c7e3fa00d4e4c-dirty
author cstrittmatter
date Thu, 21 Dec 2017 12:45:31 -0500
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1 <tool id="seqsero_v2" name="seqsero_v2" version="2.0">
2 <requirements>
3 <requirement type="package" version="2.7">python</requirement>
4 <requirement type="package">biopython</requirement>
5 <requirement type="package">blast</requirement>
6 <requirement type="package">samtools</requirement>
7 <requirement type="package">sra-tools</requirement>
8 <requirement type="package">bwa</requirement>
9 <requirement type="package">spades</requirement>
10 <requirement type="package">bedtools</requirement>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13
14 ln -s $fastq1 sample_1.fastq;
15 ln -s $fastq2 sample_2.fastq;
16
17
18
19 $__tool_directory__/SeqSero2.py
20 -p $numofthr
21 -i sample_1.fastq sample_2.fastq
22 -b $maptype;
23 cat SeqSero_result*/Seqsero_result.txt > results.txt;
24
25 ]]></command>
26 <inputs>
27
28
29
30
31 <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
32 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" />
33 <param name="numofthr" type="select" label="Number of threads">
34 <option value="1">1</option>
35 <option value="2">2</option>
36 <option value="3">3</option>
37 <option value="4">4</option>
38 </param>
39 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
40 <option value="mem">mem</option>
41 <option value="sam">sam</option>
42 </param>
43
44
45 </inputs>
46 <outputs>
47 <data format="txt" label="SeqSero Results" name="results" from_work_dir="results.txt"/>
48 </outputs>
49 <tests>
50 <test>
51 <output name="results" file="results.txt"/>
52 </test>
53 </tests>
54 <help><![CDATA[
55
56 **Usage: SeqSero2.py**
57
58 **Number of threads**
59
60 The range is 1 through 4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1
61
62 **Algorithms for BWA mapping**
63
64 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
65
66 ]]></help>
67 <citations>
68 <citation type="bibtex">
69 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
70 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
71 journal={J Clin Microbiol}, publisher={ASM},
72 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
73 year={2015}, month={Max},
74 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
75 }</citation>
76 </citations>
77
78 </tool>