Mercurial > repos > jpetteng > ectyper

comparison ecoli_serotyping/ectyper.xml @ 10:5b52b3842765 draft

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Uploaded
author jpetteng
date Sat, 06 Jan 2018 13:32:23 -0500
parents 148199949636
children 8cb863e320e7
comparison
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9:148199949636 10:5b52b3842765
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">biopython</requirement> 5 <requirement type="package">biopython</requirement>
5 <requirement type="package">blast</requirement> 6 <requirement type="package">blast</requirement>
6 <requirement type="package">samtools</requirement> 7 <requirement type="package">samtools</requirement>
7 <requirement type="package">bcftools</requirement> 8 <requirement type="package">bcftools</requirement>
8 <requirement type="package">bowtie</requirement> 9 <requirement type="package">bowtie</requirement>
17 ln -s $jobtype.fastq1 sample_1.fastq; 18 ln -s $jobtype.fastq1 sample_1.fastq;
18 #else if $jobtype.select == "pe" 19 #else if $jobtype.select == "pe"
19 ln -s $jobtype.fastq1 sample_1.fastq; 20 ln -s $jobtype.fastq1 sample_1.fastq;
20 ln -s $jobtype.fastq2 sample_2.fastq; 21 ln -s $jobtype.fastq2 sample_2.fastq;
21 #end if 22 #end if
22 PYTHONPATH=\$PATHONPATH:$__tool_directory__/ecytper/ 23 ectyper.py
23
24 $__tool_directory__/ectyper/ectyper.py
25 #if $jobtype.select == "asm" 24 #if $jobtype.select == "asm"
26 -m 4 25 -m 4
27 -i sample.fasta 26 -i sample.fasta
28 #else if $jobtype.select == "se" 27 #else if $jobtype.select == "se"
29 -m 3 28 -m 3