Mercurial > repos > estrain > seqsero2_v1_0_1

comparison seqsero2.xml @ 5:b4f4b9d54c08

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Fri, 06 Sep 2019 04:37:42 -0400
parents
children
comparison
equal deleted inserted replaced
4:92d60761a210 5:b4f4b9d54c08
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 <requirement type="package">salmid</requirement>
13 </requirements>
14 <command detect_errors="exit_code"><![CDATA[
15 echo "SeqSero 2 v. 1.0.1" ;
16 #if $reads.reads_select == 'history'
17 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
18 #set $forward = $reads.forward
19 #set $reverse = $reads.reverse
20 #else
21 #set $name = $reads.coll.name.replace(' ', '_')
22 #set $forward = $reads.coll.forward
23 #set $reverse = $reads.coll.reverse
24 #end if
25 echo $name ;
26 echo "-=-=-=-=-" ;
27 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
28 gunzip -c $forward > forward.fastq;
29 #set $forward = './forward.fastq'
30 #end if
31 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
32 gunzip -c $reverse > reverse.fastq;
33 #set $reverse = './reverse.fastq'
34 #end if
35 ln -s $forward ${name}_1.fastq;
36 ln -s $reverse ${name}_2.fastq;
37 mkdir ./output;
38 touch output/SeqSero_log.txt ;
39 python $__tool_directory__/SeqSero2_package.py
40 -p \${GALAXY_SLOTS:-4}
41 -t 2
42 -m $mode
43 -d ./output
44 #if $mode == 'a':
45 -b $maptype
46 #end if
47 -i ${name}_1.fastq ${name}_2.fastq &&
48 echo "-=-=-=-=-" &&
49 cat output/SeqSero_log.txt &&
50 echo "-=-=-=-=-" &&
51 ls -lah ./output
52 ]]></command>
53 <inputs>
54
55 <conditional name="reads">
56 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
57 <option value="collection">Paired collection from your history</option>
58 <option value="history">Two FASTQ datasets from your history</option>
59 </param>
60 <when value="collection">
61 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
62 </when>
63 <when value="history">
64 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
65 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
66 </when>
67 </conditional>
68
69 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
70 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
71 <!-- <param name="numofthr" type="select" label="Number of threads">
72 <option value="1">1</option>
73 <option value="2">2</option>
74 <option value="3">3</option>
75 <option value="4">4</option> -->
76 <!-- </param> -->
77
78 <param label="Analysis mode" type="select" name="mode">
79 <option value="a">allele mode</option>
80 <option value="k">k-mer mode</option>
81 </param>
82
83 <param name="maptype" type="select" label="Algorithms for BWA mapping">
84 <option value="mem">mem</option>
85 <option value="sam">sam</option>
86 </param>
87
88
89
90 </inputs>
91 <outputs>
92 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
93 </outputs>
94 <tests>
95 <!-- <test>
96 <param name="reads_select" value="history" />
97 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
98 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
99 <output name="results" file="Seqsero_result.tsv" />
100 </test>
101 <test>
102 <param name="reads_select" value="collection" />
103 <param name="coll">
104 <collection type="paired">
105 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
106 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
107 </collection>
108 </param>
109 <output name="results" file="Seqsero_result.tsv" />
110 </test> -->
111 <test>
112 <param name="mode" value="k" />
113 <param name="reads_select" value="history" />
114 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
115 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
116 <output name="results" file="Seqsero_result_25k.tsv" />
117 </test>
118 <test>
119 <param name="mode" value="k" />
120 <param name="reads_select" value="collection" />
121 <param name="coll">
122 <collection type="paired">
123 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
124 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
125 </collection>
126 </param>
127 <output name="results" file="Seqsero_result_25k_coll.tsv" />
128 </test>
129 <test>
130 <param name="mode" value="a" />
131 <param name="reads_select" value="history" />
132 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
133 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
134 <assert_stdout>
135 <has_text text="predicted antigenic profile does not exist" />
136 </assert_stdout>
137 </test>
138 <!-- <test>
139 <param name="mode" value="a" />
140 <param name="reads_select" value="collection" />
141 <param name="coll">
142 <collection type="paired">
143 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
144 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
145 </collection>
146 </param>
147 <output name="results" file="Seqsero_result_allele.tsv" />
148 </test> -->
149 </tests>
150 <help><![CDATA[
151
152 **Usage: SeqSero2.py**
153
154 **Algorithms for BWA mapping**
155
156 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now SeqSero2 is only optimized for "mem" mode
157
158 ]]></help>
159 <citations>
160 <citation type="bibtex">
161 @misc{zhang_yin_jones_zhang_deathrage_dinsmore_fitzgeral_fields_deng_2015,
162 title={Salmonella serotype determination utilizing high-throughput genome sequencing data.},
163 journal={J Clin Microbiol}, publisher={ASM},
164 author={Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.},
165 year={2015}, month={Max},
166 url={http://http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15}},
167 }</citation>
168 <citation type="bibtex">
169 @misc{cfsan_biostatistics_group_2017,
170 title={CFSAN Biostatistics Group fork of SeqSero2},
171 url={https://github.com/CFSAN-Biostatistics/SeqSero2.git}},
172 </citation>
173 </citations>
174
175 </tool>