Mercurial > repos > estrain > seqsero2_v1_0_1

comparison seqsero2.xml @ 35:b99f3a65254d

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author estrain
date Sat, 07 Sep 2019 15:27:43 -0400
parents 6d8f3c66a836
children 2fb62709dc5e
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34:4fcd9834e66b 35:b99f3a65254d
1 <tool id="seqsero2_v1_0_1" name="SeqSero 2" version="1.0.1"> 1 <tool id="seqsero2_v1_0_1" name="SeqSero 2" version="1.0.1">
2 <description>Salmonella serotype prediction</description> 2 <description>Salmonella serotype prediction</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.6">python</requirement> 4 <requirement type="package">biopython</requirement>
5 <requirement type="package" version="1.74">biopython</requirement> 5 <requirement type="package">blast</requirement>
6 <requirement type="package" version="2.7.1">blast</requirement> 6 <requirement type="package">samtools</requirement>
7 <requirement type="package" version="1.9">samtools</requirement> 7 <requirement type="package">sra-tools</requirement>
8 <requirement type="package" version="2.9.1">sra-tools</requirement> 8 <requirement type="package">bwa</requirement>
9 <requirement type="package" version="0.7.17">bwa</requirement> 9 <requirement type="package">spades</requirement>
10 <requirement type="package" version="3.13.1">spades</requirement> 10 <requirement type="package">bedtools</requirement>
11 <requirement type="package" version="2.27.1">bedtools</requirement>
12 </requirements> 11 </requirements>
13 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
14 echo "SeqSero 2 v. 1.0.1" ; 13 echo "SeqSero 2 v. 1.0.1" ;
15 mkdir ./output; 14 mkdir ./output;
16 15
34 #set $reverse = './reverse.fastq' 33 #set $reverse = './reverse.fastq'
35 #end if 34 #end if
36 ln -s $forward ${name}_1.fastq; 35 ln -s $forward ${name}_1.fastq;
37 ln -s $reverse ${name}_2.fastq; 36 ln -s $reverse ${name}_2.fastq;
38 touch output/SeqSero_log.txt ; 37 touch output/SeqSero_log.txt ;
39 python $__tool_directory__/SeqSero2_package.py 38 python3 $__tool_directory__/SeqSero2_package.py
40 -p \${GALAXY_SLOTS:-4} 39 -p \${GALAXY_SLOTS:-4}
41 -t 2 40 -t 2
42 -m $mode 41 -m $mode
43 -d ./output 42 -d ./output
44 #if $mode == 'a': 43 #if $mode == 'a':