Mercurial > repos > jpayne > seqsero_v2

comparison seqsero2.xml @ 14:496f5f2b5e75

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author estrain
date Tue, 14 Feb 2023 12:11:27 -0500
parents 3513b93ebe6a
children 3b6d5b60968f
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13:3513b93ebe6a 14:496f5f2b5e75
1 <tool id="seqsero_v2" name="SeqSero 2" version="2.0.1"> 1 <tool id="seqsero2v111" name="SeqSero2 v1.2.1" version="8">
2 <description>Salmonella serotype prediction</description> 2 <description>Salmonella serotype prediction</description>
3 <macros>
4 <token name="@VERSION@">1.2.1</token>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="3.6">python</requirement> 7 <requirement type="package" version="@VERSION@">seqsero2</requirement>
5 <requirement type="package" version="1.70">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 </requirements> 8 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
14 echo "SeqSero 2 v. 1.0.0" ; 10 echo "SeqSero2 v1.2.1";
11 mkdir ./output;
12
15 #if $reads.reads_select == 'history' 13 #if $reads.reads_select == 'history'
16 #set $name = $reads.forward.name.split('.')[0].replace(' ','_') 14 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
17 #set $forward = $reads.forward 15 #set $forward = $reads.forward
18 #set $reverse = $reads.reverse 16 #set $reverse = $reads.reverse
19 #else 17 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
20 #set $name = $reads.coll.name.replace(' ', '_') 18 #set $tval = 2
21 #set $forward = $reads.coll.forward 19 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
22 #set $reverse = $reads.coll.reverse 20 gunzip -c $reverse > reverse.fastq;
23 #end if 21 #set $reverse = './reverse.fastq'
24 echo $name ; 22 gunzip -c $forward > forward.fastq;
25 echo "-=-=-=-=-" ; 23 #set $forward = './forward.fastq'
26 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz') 24 #end if
27 gunzip -c $forward > forward.fastq;
28 #set $forward = './forward.fastq'
29 #end if
30 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
31 gunzip -c $reverse > reverse.fastq;
32 #set $reverse = './reverse.fastq'
33 #end if
34 ln -s $forward ${name}_1.fastq; 25 ln -s $forward ${name}_1.fastq;
35 ln -s $reverse ${name}_2.fastq; 26 ln -s $reverse ${name}_2.fastq;
36 mkdir ./output; 27 #else if $reads.reads_select == 'collection'
37 touch output/SeqSero_log.txt ; 28 #set $name = $reads.coll.name.replace(' ', '_')
38 python $__tool_directory__/SeqSero2/SeqSero2_package.py 29 #set $forward = $reads.coll.forward
39 -p \${GALAXY_SLOTS:-4} 30 #set $reverse = $reads.coll.reverse
40 -t 2 31 #set $infile = $name + "_1.fastq " + $name + "_2.fastq"
32 #set $tval = 2
33 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
34 gunzip -c $reverse > reverse.fastq;
35 #set $reverse = './reverse.fastq'
36 gunzip -c $forward > forward.fastq;
37 #set $forward = './forward.fastq'
38 #end if
39 ln -s $forward ${name}_1.fastq;
40 ln -s $reverse ${name}_2.fastq;
41 #else
42 #set $name = $reads.assembly.name.replace(' ', '_')
43 #set $ga = $reads.assembly
44 #set $infile = $name + ".fasta"
45 ln -s $ga ${name}.fasta;
46 #set $tval = 4
47 #set $mode='k'
48 #end if
49 echo $name ;
50 echo "-=-=-=-=-" ;
51 touch output/SeqSero_log.txt ;
52 SeqSero2_package.py
53 -p \${GALAXY_SLOTS:-1}
54 -t $tval
41 -m $mode 55 -m $mode
42 -d ./output 56 -d ./output
43 #if $mode == 'a': 57 #if $mode == 'a':
44 -b $maptype 58 -b $maptype
45 #end if 59 #end if
46 -i ${name}_1.fastq ${name}_2.fastq && 60 -i $infile &&
47 echo "-=-=-=-=-" && 61 echo "-=-=-=-=-" &&
48 cat output/SeqSero_log.txt && 62 cat output/SeqSero_log.txt &&
49 echo "-=-=-=-=-" && 63 echo "-=-=-=-=-" &&
50 ls -lah ./output 64 ls -lah ./output
51 ]]></command> 65 ]]></command>
52 <inputs> 66 <inputs>
53 67
54 <conditional name="reads"> 68 <conditional name="reads">
55 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> 69 <param name="reads_select" type="select" label="Genome assembly,paired-end collection, or two datasets from your history">
56 <option value="collection">Paired collection from your history</option> 70 <option value="collection">Paired collection from your history</option>
57 <option value="history">Two FASTQ datasets from your history</option> 71 <option value="history">Two FASTQ datasets from your history</option>
72 <option value="genome">Genome Assembly</option>
58 </param> 73 </param>
59 <when value="collection"> 74 <when value="collection">
60 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" /> 75 <param label="Paired reads" name="coll" type="data_collection" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" collection_type="paired" />
61 </when> 76 </when>
62 <when value="history"> 77 <when value="history">
63 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> 78 <param label="Forward reads" type="data" name="forward" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
64 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" /> 79 <param label="Reverse reads" type="data" name="reverse" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz" />
80 </when>
81 <when value="genome">
82 <param label="Genome assembly" name="assembly" type="data" format="fasta"/>
65 </when> 83 </when>
66 </conditional> 84 </conditional>
67 85
68 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" /> 86 <!-- <param name="fastq1" type="data" format="fastq" label="FASTQ paired end read 1" />
69 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> --> 87 <param name="fastq2" type="data" format="fastq" label="FASTQ paired end read 2" /> -->
73 <option value="3">3</option> 91 <option value="3">3</option>
74 <option value="4">4</option> --> 92 <option value="4">4</option> -->
75 <!-- </param> --> 93 <!-- </param> -->
76 94
77 <param label="Analysis mode" type="select" name="mode"> 95 <param label="Analysis mode" type="select" name="mode">
78 <option value="a">allele mode</option> 96 <option value="a">allele mode</option>
79 <option value="k">k-mer mode</option> 97 <option value="k">k-mer mode</option>
80 </param> 98 </param>
81 99
82 <param name="maptype" type="select" label="Algorithms for BWA mapping"> 100 <param name="maptype" type="select" label="Algorithms for BWA mapping">
83 <option value="mem">mem</option> 101 <option value="mem">mem</option>
84 <option value="sam">sam</option> 102 <option value="sam">sam</option>
86 104
87 105
88 106
89 </inputs> 107 </inputs>
90 <outputs> 108 <outputs>
91 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/Seqsero_result.tsv"/> 109 <data format="tabular" label="SeqSero Results" name="results" from_work_dir="output/SeqSero_result.tsv"/>
92 </outputs> 110 </outputs>
93 <tests> 111 <tests>
94 <!-- <test> 112 <!-- <test>
95 <param name="reads_select" value="history" /> 113 <param name="reads_select" value="history" />
96 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" /> 114 <param name="forward" value="forward.fastq.gz" ftype="fastqsanger.gz" />
129 <param name="mode" value="a" /> 147 <param name="mode" value="a" />
130 <param name="reads_select" value="history" /> 148 <param name="reads_select" value="history" />
131 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" /> 149 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
132 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" /> 150 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
133 <assert_stdout> 151 <assert_stdout>
134 <has_text text="predicted antigenic profile does not exist" /> 152 <has_text text="predicted antigenic profile does not exist" />
135 </assert_stdout> 153 </assert_stdout>
136 </test> 154 </test>
137 <!-- <test> 155 <!-- <test>
138 <param name="mode" value="a" /> 156 <param name="mode" value="a" />
139 <param name="reads_select" value="collection" /> 157 <param name="reads_select" value="collection" />