Mercurial > repos > estrain > seqsero2_v1_0_1

comparison seqsero2.xml @ 25:55d2ec45737f

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author estrain
date Sat, 07 Sep 2019 14:08:55 -0400
parents b2b1d018b90d
children 4a709def2980
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24:4e1596ee5c94 25:55d2ec45737f
10 <requirement type="package" version="3.13.1">spades</requirement> 10 <requirement type="package" version="3.13.1">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 echo "SeqSero 2 v. 1.0.1" ; 14 echo "SeqSero 2 v. 1.0.1" ;
15 cp $__tool_directory__/SalmID.py .;
16 cp $__tool_directory__/invA_mers_dict .;
17 cp $__tool_directory__/rpoB_mers_dict .;
18 15
19 #if $reads.reads_select == 'history' 16 #if $reads.reads_select == 'history'
20 #set $name = $reads.forward.name.split('.')[0].replace(' ','_') 17 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
21 #set $forward = $reads.forward 18 #set $forward = $reads.forward
22 #set $reverse = $reads.reverse 19 #set $reverse = $reads.reverse
37 #end if 34 #end if
38 ln -s $forward ${name}_1.fastq; 35 ln -s $forward ${name}_1.fastq;
39 ln -s $reverse ${name}_2.fastq; 36 ln -s $reverse ${name}_2.fastq;
40 mkdir ./output; 37 mkdir ./output;
41 touch output/SeqSero_log.txt ; 38 touch output/SeqSero_log.txt ;
39 python $__tool_directory__/SalmID.py -i ${name}_1.fastq > salmid_output.txt;
42 python $__tool_directory__/SeqSero2_package.py 40 python $__tool_directory__/SeqSero2_package.py
43 -p \${GALAXY_SLOTS:-4} 41 -p \${GALAXY_SLOTS:-4}
44 -t 2 42 -t 2
45 -m $mode 43 -m $mode
46 -d ./output 44 -d ./output