Mercurial > repos > jpayne > seqsero_v2

comparison seqsero2.xml @ 0:4ff2aee11e5b

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author jpayne
date Tue, 06 Nov 2018 09:45:57 -0500
parents
children fae43708974d
comparison
equal deleted inserted replaced
-1:000000000000 0:4ff2aee11e5b
1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0">
2 <description>Salmonella serotype prediction</description>
3 <requirements>
4 <requirement type="package" version="2.7.10">python</requirement>
5 <requirement type="package" version="1.60">biopython</requirement>
6 <requirement type="package" version="2.2.31">blast</requirement>
7 <requirement type="package" version="1.9">samtools</requirement>
8 <requirement type="package" version="2.6.2">sra-tools</requirement>
9 <requirement type="package" version="0.7.17">bwa</requirement>
10 <requirement type="package" version="3.9.0">spades</requirement>
11 <requirement type="package" version="2.27.1">bedtools</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[
14 #if $reads.reads_select == 'history'
15 #set name = $reads.forward.name.split('_')[0]
16 #set forward = $reads.forward
17 #set reverse = $reads.reverse
18 #else
19 #set name = $reads.coll.name
20 #set forward = $reads.coll.forward
21 #set reverse = $reads.coll.reverse
22 #end if
23 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz')
24 gunzip -c $forward > forward.fastq;
25 #set forward = './forward.fastq'
26 #end if
27 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
28 gunzip -c $reverse > reverse.fastq;
29 #set reverse = './reverse.fastq'
30 #end if
31 ln -s forward.fastq ${name}_1.fastq;
32 ln -s reverse.fastq ${name}_2.fastq;
33 $__tool_directory__/SeqSero2.py
34 -p \${GALAXY_SLOTS:-4}
35 -i ${name}_1.fastq ${name}_2.fastq
36 -b $maptype &&
37 cat SeqSero_result*/Seqsero_result.tsv > results.tsv
38
39 ]]></command>
40 <inputs>
41
42
43 <conditional name="reads">
44 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
45 <option value="collection">Paired collection from your history</option>
46 <option value="history">Two FASTQ datasets from your history</option>
47 </param>
48 <when value="collection">
49 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
50 </when>
51 <when value="history">
52 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
53 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
54 </when>
55 </conditional>
56
57 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
58 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
59 <!-- <param name="numofthr" type="select" label="Number of threads">
60 <option value="1">1</option>
61 <option value="2">2</option>
62 <option value="3">3</option>
63 <option value="4">4</option> -->
64 <!-- </param> -->
65 <param name="maptype" type="select" label="Algorithms for BWA mapping?">
66 <option value="mem">mem</option>
67 <option value="sam">sam</option>
68 </param>
69
70
71 </inputs>
72 <outputs>
73 <data format="tsv" label="SeqSero Results" name="results" from_work_dir="results.tsv"/>
74 </outputs>
75 <tests>
76 <test>
77 <param name="reads_select" value="history" />
78 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
79 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
80 </test>
81 <test>
82 <param name="reads_select" value="collection" />
83 <param name="coll">
84 <collection type="paired">
85 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
86 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
87 </collection>
88 </param>
89 </test>
90 </tests>
91 <help><![CDATA[
92
93 **Usage: SeqSero2.py**
94
95 **Algorithms for BWA mapping**
96
97 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
98
99 ]]></help>
100 <citations>
101 <citation type="bibtex">
102 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
103 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
104 journal={J Clin Microbiol}, publisher={ASM},
105 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
106 year={2015}, month={Max},
107 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
108 }</citation>
109 </citations>
110
111 </tool>