Mercurial > repos > jpayne > seqsero_v2

comparison seqsero2.xml @ 12:4ac593d4b40f

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planemo upload
author jpayne
date Wed, 14 Aug 2019 17:45:41 -0400
parents f6f0702de3b4
children 3513b93ebe6a
comparison
equal deleted inserted replaced
11:f6f0702de3b4 12:4ac593d4b40f
5 <requirement type="package" version="1.70">biopython</requirement> 5 <requirement type="package" version="1.70">biopython</requirement>
6 <requirement type="package" version="2.7.1">blast</requirement> 6 <requirement type="package" version="2.7.1">blast</requirement>
7 <requirement type="package" version="1.9">samtools</requirement> 7 <requirement type="package" version="1.9">samtools</requirement>
8 <requirement type="package" version="2.9.1">sra-tools</requirement> 8 <requirement type="package" version="2.9.1">sra-tools</requirement>
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="3.13.1">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. 1.0.0" ; 14 echo "SeqSero 2 v. 1.0.0" ;
15 #if $reads.reads_select == 'history' 15 #if $reads.reads_select == 'history'
32 #set $reverse = './reverse.fastq' 32 #set $reverse = './reverse.fastq'
33 #end if 33 #end if
34 ln -s $forward ${name}_1.fastq; 34 ln -s $forward ${name}_1.fastq;
35 ln -s $reverse ${name}_2.fastq; 35 ln -s $reverse ${name}_2.fastq;
36 mkdir ./output; 36 mkdir ./output;
37 touch output/SeqSero_log.txt ;
37 python $__tool_directory__/SeqSero2/SeqSero2_package.py 38 python $__tool_directory__/SeqSero2/SeqSero2_package.py
38 -p \${GALAXY_SLOTS:-4} 39 -p \${GALAXY_SLOTS:-4}
39 -t 2 40 -t 2
40 -m $mode 41 -m $mode
41 -d ./output 42 -d ./output
125 <output name="results" file="Seqsero_result_25k_coll.tsv" /> 126 <output name="results" file="Seqsero_result_25k_coll.tsv" />
126 </test> 127 </test>
127 <test> 128 <test>
128 <param name="mode" value="a" /> 129 <param name="mode" value="a" />
129 <param name="reads_select" value="history" /> 130 <param name="reads_select" value="history" />
130 <param name="forward" value="forward_25k.fastq.gz" ftype="fastqsanger" /> 131 <param name="forward" value="forward_250k.fastq.gz" ftype="fastqsanger" />
131 <param name="reverse" value="reverse_25k.fastq.gz" ftype="fastqsanger" /> 132 <param name="reverse" value="reverse_250k.fastq.gz" ftype="fastqsanger" />
132 <output name="results" file="Seqsero_result_25k.tsv" /> 133 <assert_stdout>
134 <has_text text="predicted antigenic profile does not exist" />
135 </assert_stdout>
133 </test> 136 </test>
134 <!-- <test> 137 <!-- <test>
135 <param name="mode" value="a" /> 138 <param name="mode" value="a" />
136 <param name="reads_select" value="collection" /> 139 <param name="reads_select" value="collection" />
137 <param name="coll"> 140 <param name="coll">