Mercurial > repos > estrain > seqsero2_v1_0_1

comparison seqsero2.xml @ 27:4a709def2980

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author estrain
date Sat, 07 Sep 2019 14:20:44 -0400
parents 55d2ec45737f
children 67621118a465
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26:2bc92eaf2844 27:4a709def2980
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 mkdir ./output;
16 cp $__tool_directory__/SalmID.py output/;
17 cp $__tool_directory__/invA_mers_dict output/;
18 cp $__tool_directory__/rpoB_mers.dict output/;
15 19
16 #if $reads.reads_select == 'history' 20 #if $reads.reads_select == 'history'
17 #set $name = $reads.forward.name.split('.')[0].replace(' ','_') 21 #set $name = $reads.forward.name.split('.')[0].replace(' ','_')
18 #set $forward = $reads.forward 22 #set $forward = $reads.forward
19 #set $reverse = $reads.reverse 23 #set $reverse = $reads.reverse
20 #else 24 #else
21 #set $name = $reads.coll.name.replace(' ', '_') 25 #set $name = $reads.coll.name.replace(' ', '_')
22 #set $forward = $reads.coll.forward 26 #set $forward = $reads.coll.forward
23 #set $reverse = $reads.coll.reverse 27 #set $reverse = $reads.coll.reverse
24 #end if 28 #end if
25 echo $name ; 29 echo $name ;
26 echo "-=-=-=-=-" ; 30 echo "-=-=-=-=-" ;
27 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz') 31 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
28 gunzip -c $forward > forward.fastq; 32 gunzip -c $forward > forward.fastq;
29 #set $forward = './forward.fastq' 33 #set $forward = './forward.fastq'
30 #end if 34 #end if
31 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz') 35 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
32 gunzip -c $reverse > reverse.fastq; 36 gunzip -c $reverse > reverse.fastq;
33 #set $reverse = './reverse.fastq' 37 #set $reverse = './reverse.fastq'
34 #end if 38 #end if
35 ln -s $forward ${name}_1.fastq; 39 ln -s $forward ${name}_1.fastq;
36 ln -s $reverse ${name}_2.fastq; 40 ln -s $reverse ${name}_2.fastq;
37 mkdir ./output; 41 touch output/SeqSero_log.txt ;
38 touch output/SeqSero_log.txt ; 42 python $__tool_directory__/SeqSero2_package.py
39 python $__tool_directory__/SalmID.py -i ${name}_1.fastq > salmid_output.txt;
40 python $__tool_directory__/SeqSero2_package.py
41 -p \${GALAXY_SLOTS:-4} 43 -p \${GALAXY_SLOTS:-4}
42 -t 2 44 -t 2
43 -m $mode 45 -m $mode
44 -d ./output 46 -d ./output
45 #if $mode == 'a': 47 #if $mode == 'a':