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comparison seqsero.xml @ 3:ff697abc6b11 draft

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author estrain
date Wed, 11 Sep 2019 06:50:04 -0400
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2:2f81c626194a 3:ff697abc6b11
1 <tool id="seqsero_v1" name="seqsero_v1" version="1.0">
2 <requirements>
3 <requirement type="package" version="2.7">python</requirement>
4 <requirement type="package" version="1.65">biopython</requirement>
5 <requirement type="package" version="2.7.1">blast</requirement>
6 <requirement type="package" version="1.9">samtools</requirement>
7 <requirement type="package" version="2.9.1">sra-tools</requirement>
8 <requirement type="package" version="0.7.17">bwa</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 #if $jobtype.select == "asm"
12 ln -s $jobtype.draft sample.fasta;
13 #else if $jobtype.select == "se"
14 ln -s $jobtype.fastq1 sample_1.fastq;
15 #else if $jobtype.select == "pe"
16 ln -s $jobtype.fastq1 sample_1.fastq;
17 ln -s $jobtype.fastq2 sample_2.fastq;
18 #end if
19
20 $__tool_directory__/SeqSero.py
21 #if $jobtype.select == "asm"
22 -m 4
23 -i sample.fasta
24 #else if $jobtype.select == "se"
25 -m 3
26 -i sample_1.fastq
27 #else if $jobtype.select == "pe"
28 -m 2
29 -i sample_1.fastq sample_2.fastq
30 #end if
31 -b $maptype.select
32 ; cat SeqSero_result*/Seqsero_result.txt > results.txt;
33
34 ]]></command>
35 <inputs>
36 <conditional name="jobtype">
37 <param name="select" type="select" label="Assembly or FASTQ Reads?">
38 <option value="asm">Genome Assembly</option>
39 <option value="se">Single-End Reads</option>
40 <option value="pe">Paired-End Reads</option>
41 </param>
42 <when value="asm">
43 <param name="draft" type="data" format="fasta" label="FASTA" />
44 </when>
45 <when value="se">
46 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
47 </when>
48 <when value="pe">
49 <param name="fastq1" type="data" format="fastq" label="FASTQ" />
50 <param name="fastq2" type="data" format="fastq" label="FASTQ" />
51 </when>
52 </conditional>
53
54 <conditional name="maptype">
55 <param name="select" type="select" label="Algorithms for BWA mapping?">
56 <option value="sam">sam</option>
57 <option value="mem">mem</option>
58 </param>
59 </conditional>
60
61 </inputs>
62 <outputs>
63 <data format="txt" label="SeqSero Results" name="results" from_work_dir="results.txt"/>
64 </outputs>
65 <help><![CDATA[
66
67 ]]></help>
68 <citations>
69 <citation type="bibtex">
70 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
71 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
72 journal={J Clin Microbiol}, publisher={ASM},
73 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
74 year={2015}, month={Max},
75 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
76 }</citation>
77 </citations>
78
79 </tool>