Mercurial > repos > jpayne > seqsero_v2

comparison seqsero2.xml @ 3:b18e8cdfdf81

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planemo upload
author jpayne
date Tue, 13 Nov 2018 16:18:17 -0500
parents 15572bf93a2a
children b82e5f3c9187
comparison
equal deleted inserted replaced
2:15572bf93a2a 3:b18e8cdfdf81
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="3.12.0">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].replace(' ','_') 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.replace(' ', '_') 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 echo $name ;
24 echo "-=-=-=-=-" ; 24 echo "-=-=-=-=-" ;
25 #if forward.is_of_type('fastq.gz', 'fastqsanger.gz'): 25 #if $forward.is_of_type('fastq.gz', 'fastqsanger.gz')
26 gunzip -c $forward > forward.fastq; 26 gunzip -c $forward > forward.fastq;
27 #set forward = './forward.fastq' 27 #set $forward = './forward.fastq'
28 #end if 28 #end if
29 #if reverse.is_of_type('fastq.gz', 'fastqsanger.gz'): 29 #if $reverse.is_of_type('fastq.gz', 'fastqsanger.gz')
30 gunzip -c $reverse > reverse.fastq; 30 gunzip -c $reverse > reverse.fastq;
31 #set reverse = './reverse.fastq' 31 #set $reverse = './reverse.fastq'
32 #end if 32 #end if
33 ln -s forward.fastq ${name}_1.fastq; 33 ln -s $forward ${name}_1.fastq;
34 ln -s reverse.fastq ${name}_2.fastq; 34 ln -s $reverse ${name}_2.fastq;
35 mkdir ./output; 35 mkdir ./output;
36 python $__tool_directory__/SeqSero2/SeqSero2_package.py 36 python $__tool_directory__/SeqSero2/SeqSero2_package.py
37 -p \${GALAXY_SLOTS:-4} 37 -p \${GALAXY_SLOTS:-4}
38 -t 2 38 -t 2
39 -m $mode 39 -m $mode
40 -d ./output 40 -d ./output
106 <output name="results" file="Seqsero_result.tsv" /> 106 <output name="results" file="Seqsero_result.tsv" />
107 </test> --> 107 </test> -->
108 <test> 108 <test>
109 <param name="mode" value="k" /> 109 <param name="mode" value="k" />
110 <param name="reads_select" value="history" /> 110 <param name="reads_select" value="history" />
111 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger.gz" /> 111 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" />
112 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger.gz" /> 112 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" />
113 <output name="results" file="Seqsero_result_25k.tsv" /> 113 <output name="results" file="Seqsero_result_25k.tsv" />
114 </test> 114 </test>
115 <test> 115 <test>
116 <param name="mode" value="k" /> 116 <param name="mode" value="k" />
117 <param name="reads_select" value="collection" /> 117 <param name="reads_select" value="collection" />