|
jpayne@0
|
1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
|
|
jpayne@0
|
2 <description>into a multi-sample VCF with consensus SNPs</description>
|
|
jpayne@0
|
3 <requirements>
|
|
jpayne@62
|
4 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
|
|
jpayne@61
|
5 <requirement type="package" version="1.9">bcftools</requirement>
|
|
jpayne@58
|
6 <requirement type="package" version="1.0.8">bzip2</requirement>
|
|
jpayne@58
|
7 <requirement type="package" version="2.2.1">snp-pipeline</requirement>
|
|
jpayne@58
|
8 <requirement type="package" version="0.2.6">tabix</requirement>
|
|
jpayne@61
|
9 <requirement type="package" version="1.9">htslib</requirement>
|
|
jpayne@58
|
10 <!-- <requirement type="package" version="3.6.8">python</requirement> -->
|
|
jpayne@0
|
11 </requirements>
|
|
jpayne@0
|
12 <command detect_errors="exit_code"><![CDATA[
|
|
jpayne@28
|
13 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
|
|
jpayne@9
|
14 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
|
|
jpayne@0
|
15 #for $vcf in $vcfs
|
|
jpayne@0
|
16 -n $vcf.element_identifier -f $vcf
|
|
jpayne@0
|
17 #end for
|
|
jpayne@0
|
18 > ./file
|
|
jpayne@0
|
19 && cat ./file
|
|
jpayne@56
|
20 && cfsan_snp_pipeline merge_vcfs ./file
|
|
jpayne@0
|
21 ]]></command>
|
|
jpayne@0
|
22 <inputs>
|
|
jpayne@0
|
23 <param type="data_collection" format="vcf" collection_type="list" name="vcfs" label="List of VCFs" />
|
|
jpayne@0
|
24 </inputs>
|
|
jpayne@0
|
25 <outputs>
|
|
jpayne@0
|
26 <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
|
|
jpayne@0
|
27 </outputs>
|
|
jpayne@0
|
28 <tests>
|
|
jpayne@0
|
29 <test>
|
|
jpayne@0
|
30 <param name="vcfs">
|
|
jpayne@0
|
31 <collection type="list">
|
|
jpayne@0
|
32 <element name="sample1" value="samples/sample1/consensus.vcf" />
|
|
jpayne@0
|
33 <element name="sample2" value="samples/sample2/consensus.vcf" />
|
|
jpayne@0
|
34 <element name="sample3" value="samples/sample3/consensus.vcf" />
|
|
jpayne@0
|
35 <element name="sample4" value="samples/sample4/consensus.vcf" />
|
|
jpayne@0
|
36 </collection>
|
|
jpayne@0
|
37 </param>
|
|
jpayne@50
|
38 <output name="snpmav" value="snpma.vcf" lines_diff="4" />
|
|
jpayne@0
|
39 </test>
|
|
jpayne@0
|
40 </tests>
|
|
jpayne@0
|
41 <help><![CDATA[
|
|
jpayne@0
|
42 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
|
|
jpayne@0
|
43 ]]></help>
|
|
jpayne@0
|
44 <citations>
|
|
jpayne@0
|
45 <citation type="doi">10.7717/peerj-cs.20</citation>
|
|
jpayne@0
|
46 </citations>
|
|
jpayne@0
|
47 </tool> |
