Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 29:5442b9d2e5d1 draft

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Uploaded
author jpetteng
date Tue, 09 Jan 2018 11:02:23 -0500
parents 41301e1f075a
children
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28:41301e1f075a 29:5442b9d2e5d1
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">ectyper</requirement> 4 <requirement type="package">ectyper</requirement>
5 <requirement type="package">biopython</requirement>
6 <requirement type="package">blast</requirement>
7 <requirement type="package">samtools</requirement>
8 <requirement type="package">bcftools</requirement>
9 <requirement type="package">bowtie</requirement>
10 <requirement type="package">spades</requirement>
11 <requirement type="package">seqtk</requirement>
12 <requirement type="package">pandas</requirement>
13 <requirement type="package">mash</requirement>
5 </requirements> 14 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
7 #if $jobtype.select == "asm" 16 #if $jobtype.select == "asm"
8 ln -s $jobtype.draft sample.fasta; 17 ln -s $jobtype.draft sample.fasta;
9 #else if $jobtype.select == "se" 18 #else if $jobtype.select == "se"