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comparison seqsero2.xml @ 1:fae43708974d

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planemo upload
author jpayne
date Fri, 09 Nov 2018 11:30:45 -0500
parents 4ff2aee11e5b
children 15572bf93a2a
comparison
equal deleted inserted replaced
0:4ff2aee11e5b 1:fae43708974d
1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0"> 1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0">
2 <description>Salmonella serotype prediction</description> 2 <description>Salmonella serotype prediction</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7.10">python</requirement> 4 <requirement type="package" version="3.6">python</requirement>
5 <requirement type="package" version="1.60">biopython</requirement> 5 <requirement type="package" version="1.70">biopython</requirement>
6 <requirement type="package" version="2.2.31">blast</requirement> 6 <requirement type="package" version="2.7.1">blast</requirement>
7 <requirement type="package" version="1.9">samtools</requirement> 7 <requirement type="package" version="1.9">samtools</requirement>
8 <requirement type="package" version="2.6.2">sra-tools</requirement> 8 <requirement type="package" version="2.9.1">sra-tools</requirement>
9 <requirement type="package" version="0.7.17">bwa</requirement> 9 <requirement type="package" version="0.7.17">bwa</requirement>
10 <requirement type="package" version="3.9.0">spades</requirement> 10 <requirement type="package" version="3.12.0">spades</requirement>
11 <requirement type="package" version="2.27.1">bedtools</requirement> 11 <requirement type="package" version="2.27.1">bedtools</requirement>
12 </requirements> 12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 13 <command detect_errors="exit_code"><![CDATA[
14 #if $reads.reads_select == 'history' 14 #if $reads.reads_select == 'history'
15 #set name = $reads.forward.name.split('_')[0] 15 #set name = $reads.forward.name.split('.')[0].replace(' ','_')
16 #set forward = $reads.forward 16 #set forward = $reads.forward
17 #set reverse = $reads.reverse 17 #set reverse = $reads.reverse
18 #else 18 #else
19 #set name = $reads.coll.name 19 #set name = $reads.coll.name.replace(' ', '_')
20 #set forward = $reads.coll.forward 20 #set forward = $reads.coll.forward
21 #set reverse = $reads.coll.reverse 21 #set reverse = $reads.coll.reverse
22 #end if 22 #end if
23 echo $name ;
23 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz') 24 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz')
24 gunzip -c $forward > forward.fastq; 25 gunzip -c $forward > forward.fastq;
25 #set forward = './forward.fastq' 26 #set forward = './forward.fastq'
26 #end if 27 #end if
27 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz') 28 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
28 gunzip -c $reverse > reverse.fastq; 29 gunzip -c $reverse > reverse.fastq;
29 #set reverse = './reverse.fastq' 30 #set reverse = './reverse.fastq'
30 #end if 31 #end if
31 ln -s forward.fastq ${name}_1.fastq; 32 ln -s forward.fastq ${name}_1.fastq;
32 ln -s reverse.fastq ${name}_2.fastq; 33 ln -s reverse.fastq ${name}_2.fastq;
33 $__tool_directory__/SeqSero2.py 34 mkdir ./output;
35 python $__tool_directory__/SeqSero2/SeqSero2_package.py
34 -p \${GALAXY_SLOTS:-4} 36 -p \${GALAXY_SLOTS:-4}
35 -i ${name}_1.fastq ${name}_2.fastq 37 -t 2
36 -b $maptype && 38 -m $mode
37 cat SeqSero_result*/Seqsero_result.tsv > results.tsv 39 -d ./output
38 40 -b $maptype
41 -i ${name}_1.fastq ${name}_2.fastq &&
42 echo "-=-=-=-=-" &&
43 cat output/SeqSero_log.txt &&
44 echo "-=-=-=-=-" &&
45 ls -lah ./output
39 ]]></command> 46 ]]></command>
40 <inputs> 47 <inputs>
41 48
49 <param label="Analysis mode" type="select" name="mode">
50 <option value="k">k-mer mode</option>
51 <option value="a">allele mode</option>
52 </param>
42 53
43 <conditional name="reads"> 54 <conditional name="reads">
44 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> 55 <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> 56 <option value="collection">Paired collection from your history</option>
46 <option value="history">Two FASTQ datasets from your history</option> 57 <option value="history">Two FASTQ datasets from your history</option>
68 </param> 79 </param>
69 80
70 81
71 </inputs> 82 </inputs>
72 <outputs> 83 <outputs>
73 <data format="tsv" label="SeqSero Results" name="results" from_work_dir="results.tsv"/> 84 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/>
74 </outputs> 85 </outputs>
75 <tests> 86 <tests>
87 <!-- <test>
88 <param name="reads_select" value="history" />
89 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
90 <param name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
91 <output name="results" file="Seqsero_result.tsv" />
92 </test>
76 <test> 93 <test>
94 <param name="reads_select" value="collection" />
95 <param name="coll">
96 <collection type="paired">
97 <element name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
98 <element name="reverse" value="reverse.fastq.gz" ftype="fastqsanger.gz" />
99 </collection>
100 </param>
101 <output name="results" file="Seqsero_result.tsv" />
102 </test> -->
103 <test>
104 <param name="mode" value="k" />
77 <param name="reads_select" value="history" /> 105 <param name="reads_select" value="history" />
78 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" /> 106 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
79 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> 107 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
108 <output name="results" file="Seqsero_result_25k.tsv" />
80 </test> 109 </test>
81 <test> 110 <test>
111 <param name="mode" value="k" />
82 <param name="reads_select" value="collection" /> 112 <param name="reads_select" value="collection" />
83 <param name="coll"> 113 <param name="coll">
84 <collection type="paired"> 114 <collection type="paired">
85 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" /> 115 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
86 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> 116 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
87 </collection> 117 </collection>
88 </param> 118 </param>
119 <output name="results" file="Seqsero_result_25k_coll.tsv" />
89 </test> 120 </test>
121 <!-- <test>
122 <param name="mode" value="a" />
123 <param name="reads_select" value="collection" />
124 <param name="coll">
125 <collection type="paired">
126 <element name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" />
127 <element name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" />
128 </collection>
129 </param>
130 <output name="results" file="Seqsero_result_allele.tsv" />
131 </test> -->
90 </tests> 132 </tests>
91 <help><![CDATA[ 133 <help><![CDATA[
92 134
93 **Usage: SeqSero2.py** 135 **Usage: SeqSero2.py**
94 136