Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 28:41301e1f075a draft

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Uploaded
author jpetteng
date Tue, 09 Jan 2018 10:38:16 -0500
parents 54ae509ceeef
children 5442b9d2e5d1
comparison
equal deleted inserted replaced
27:c74c953c6b06 28:41301e1f075a
1 <tool id="ectyper" name="ectyper" version="2.0"> 1 <tool id="ectyper" name="ectyper" version="2.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="3.6.3">python</requirement> 3 <requirement type="package" version="3.6.3">python</requirement>
4 <requirement type="package">biopython</requirement> 4 <requirement type="package">ectyper</requirement>
5 <requirement type="package">blast</requirement>
6 <requirement type="package">samtools</requirement>
7 <requirement type="package">bcftools</requirement>
8 <requirement type="package">bowtie</requirement>
9 <requirement type="package">spades</requirement>
10 <requirement type="package">seqtk</requirement>
11 <requirement type="package">pandas</requirement>
12 <requirement type="package">mash</requirement>
13 </requirements> 5 </requirements>
14 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
15 #if $jobtype.select == "asm" 7 #if $jobtype.select == "asm"
16 ln -s $jobtype.draft sample.fasta; 8 ln -s $jobtype.draft sample.fasta;
17 #else if $jobtype.select == "se" 9 #else if $jobtype.select == "se"
19 #else if $jobtype.select == "pe" 11 #else if $jobtype.select == "pe"
20 ln -s $jobtype.fastq1 sample_1.fastq; 12 ln -s $jobtype.fastq1 sample_1.fastq;
21 ln -s $jobtype.fastq2 sample_2.fastq; 13 ln -s $jobtype.fastq2 sample_2.fastq;
22 #end if 14 #end if
23 15
24 python $__tool_directory__/ectyper/ectyper.py 16 python $__tool_directory__/bin/ectyper
25 #if $jobtype.select == "asm" 17 #if $jobtype.select == "asm"
26 -m 4 18 -m 4
27 -i sample.fasta 19 -i sample.fasta
28 #else if $jobtype.select == "se" 20 #else if $jobtype.select == "se"
29 -m 3 21 -m 3