Mercurial > repos > jpayne > snp_pipeline
annotate 6_merge_vcfs.xml @ 20:baf9ccfae6f0
planemo upload commit 7f6183b769772449fbcee903686b8d5ec5b7439f-dirty
| author | jpayne |
|---|---|
| date | Wed, 31 Jan 2018 12:45:53 -0500 |
| parents | 4bb7e4a360bc |
| children | 46b274d082a9 |
| rev | line source |
|---|---|
| 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@19 | 4 <requirement type="package" version="1.6">bcftools</requirement> |
| jpayne@12 | 5 <requirement type="package" version="1.0.6">bzip2</requirement> |
| jpayne@0 | 6 <requirement type="package" version="1.0.1">snp-pipeline</requirement> |
| jpayne@0 | 7 <requirement type="package">tabix</requirement> |
| jpayne@10 | 8 <requirement type="package" version="3.4">python3</requirement> |
| jpayne@0 | 9 </requirements> |
| jpayne@0 | 10 <command detect_errors="exit_code"><![CDATA[ |
| jpayne@20 | 11 env && |
| jpayne@20 | 12 which bcftools && |
| jpayne@20 | 13 which bunzip && |
| jpayne@20 | 14 which snp-pipeline && |
| jpayne@20 | 15 which python && |
| jpayne@20 | 16 ldconfig -p | grep "libbz2.so*" && |
| jpayne@9 | 17 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf" |
| jpayne@0 | 18 #for $vcf in $vcfs |
| jpayne@0 | 19 -n $vcf.element_identifier -f $vcf |
| jpayne@0 | 20 #end for |
| jpayne@0 | 21 > ./file |
| jpayne@0 | 22 && cat ./file |
| jpayne@0 | 23 && cfsan_snp_pipeline merge_vcfs ./file |
| jpayne@0 | 24 ]]></command> |
| jpayne@0 | 25 <inputs> |
| jpayne@0 | 26 <param type="data_collection" format="vcf" collection_type="list" name="vcfs" label="List of VCFs" /> |
| jpayne@0 | 27 </inputs> |
| jpayne@0 | 28 <outputs> |
| jpayne@0 | 29 <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/> |
| jpayne@0 | 30 </outputs> |
| jpayne@0 | 31 <tests> |
| jpayne@0 | 32 <test> |
| jpayne@0 | 33 <param name="vcfs"> |
| jpayne@0 | 34 <collection type="list"> |
| jpayne@0 | 35 <element name="sample1" value="samples/sample1/consensus.vcf" /> |
| jpayne@0 | 36 <element name="sample2" value="samples/sample2/consensus.vcf" /> |
| jpayne@0 | 37 <element name="sample3" value="samples/sample3/consensus.vcf" /> |
| jpayne@0 | 38 <element name="sample4" value="samples/sample4/consensus.vcf" /> |
| jpayne@0 | 39 </collection> |
| jpayne@0 | 40 </param> |
| jpayne@0 | 41 <output name="snpmav" value="snpma.vcf" lines_diff="2" /> |
| jpayne@0 | 42 </test> |
| jpayne@0 | 43 </tests> |
| jpayne@0 | 44 <help><![CDATA[ |
| jpayne@0 | 45 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> |
| jpayne@0 | 46 ]]></help> |
| jpayne@0 | 47 <citations> |
| jpayne@0 | 48 <citation type="doi">10.7717/peerj-cs.20</citation> |
| jpayne@0 | 49 </citations> |
| jpayne@0 | 50 </tool> |