Mercurial > repos > jpayne > snp_pipeline
comparison 5_call_consensus.xml @ 0:eefdd97a6749
planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
| author | jpayne |
|---|---|
| date | Wed, 24 Jan 2018 14:18:21 -0500 |
| parents | |
| children | 62191abf5426 |
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| -1:000000000000 | 0:eefdd97a6749 |
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| 1 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10"> | |
| 2 <description>for a sample, or lookup cached consensus SNP calls</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.0.1">snp-pipeline</requirement> | |
| 5 <requirement type="package" version="1.5.11">boto3</requirement> | |
| 6 </requirements> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 #set $identifier = $call_pileup.name.split(' ')[0] | |
| 9 $__tool_directory__/snp-cache.py snp_consenus_calls | |
| 10 "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)" | |
| 11 -c " | |
| 12 mkdir ./$identifier/ | |
| 13 && cp $call_pileup ./$identifier/reads.all.pileup | |
| 14 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta | |
| 15 " | |
| 16 -l $cache_log | |
| 17 | tar zvx ./ | |
| 18 && cp ./consensus.fasta $calls_consensus_fa | |
| 19 && cp ./consensus.vcf $calls_consensus_vcf | |
| 20 && cat $cache_log | |
| 21 ]]></command> | |
| 22 <inputs> | |
| 23 <param type="data" name="snps" format="txt" /> | |
| 24 <param type="data" name="calls" format="vcf" /> | |
| 25 <param type="data" name="call_pileup" format="pileup" /> | |
| 26 </inputs> | |
| 27 <outputs> | |
| 28 <data label="${calls.name.split(' ')[0]} consensus SNPs (VCF)" name="calls_consensus_vcf" format="vcf" /> | |
| 29 <data label="${calls.name.split(' ')[0]} consensus SNPs (FASTA)" name="calls_consensus_fa" format="fasta" hidden="true"/> | |
| 30 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" /> | |
| 31 </outputs> | |
| 32 <tests> | |
| 33 <test> | |
| 34 <param name="snps" value="snplist.txt" /> | |
| 35 <param name="calls" value="samples/sample1/var.flt.vcf" /> | |
| 36 <param name="call_pileup" value="samples/sample1/reads.all.pileup" /> | |
| 37 <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="6" /> | |
| 38 <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" /> | |
| 39 </test> | |
| 40 </tests> | |
| 41 <help><![CDATA[ | |
| 42 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> | |
| 43 ]]></help> | |
| 44 <citations> | |
| 45 <citation type="doi">10.7717/peerj-cs.20</citation> | |
| 46 </citations> | |
| 47 </tool> |