jpayne@0: <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
jpayne@0:     <description>for a sample, or lookup cached consensus SNP calls</description>
jpayne@0:     <requirements>
jpayne@0:         <requirement type="package" version="1.0.1">snp-pipeline</requirement>
jpayne@0:         <requirement type="package" version="1.5.11">boto3</requirement>
jpayne@9:         <requirement type="package" version="3.4">python</requirement>
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@0:         #set $identifier = $call_pileup.name.split(' ')[0]
jpayne@9:         python $__tool_directory__/snp-cache.py snp_consenus_calls
jpayne@0:             "\$(md5sum $snps $calls $call_pileup | cut -c -32 | md5sum | cut -c -32)"
jpayne@0:             -c "
jpayne@0:                 mkdir ./$identifier/
jpayne@0:                 && cp $call_pileup ./$identifier/reads.all.pileup
jpayne@0:                 && cfsan_snp_pipeline call_consensus -v 4 -l $snps --vcfFileName "consensus.vcf" ./$identifier/reads.all.pileup 1>&2 && tar zcv ./consensus.vcf ./consensus.fasta
jpayne@0:             "
jpayne@0:             -l $cache_log
jpayne@0:             | tar zvx ./
jpayne@0:             && cp ./consensus.fasta $calls_consensus_fa
jpayne@0:             && cp ./consensus.vcf $calls_consensus_vcf
jpayne@0:             && cat $cache_log
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <param type="data" name="snps" format="txt" />
jpayne@0:         <param type="data" name="calls" format="vcf" />
jpayne@0:         <param type="data" name="call_pileup" format="pileup" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:         <data label="${calls.name.split(' ')[0]} consensus SNPs (VCF)" name="calls_consensus_vcf" format="vcf" />
jpayne@0:         <data label="${calls.name.split(' ')[0]} consensus SNPs (FASTA)" name="calls_consensus_fa" format="fasta" hidden="true"/>
jpayne@0:         <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
jpayne@0:     </outputs>
jpayne@0:     <tests>
jpayne@0:         <test>
jpayne@0:             <param name="snps" value="snplist.txt" />
jpayne@0:             <param name="calls" value="samples/sample1/var.flt.vcf" />
jpayne@0:             <param name="call_pileup" value="samples/sample1/reads.all.pileup" />
jpayne@0:             <output name="calls_consensus_vcf" value="samples/sample1/consensus.vcf" lines_diff="6" />
jpayne@0:             <output name="calls_consensus_fa" value="samples/sample1/consensus.fasta" lines_diff="2" />
jpayne@0:         </test>
jpayne@0:     </tests>
jpayne@0:     <help><![CDATA[
jpayne@0:         <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
jpayne@0:     ]]></help>
jpayne@0:     <citations>
jpayne@0:         <citation type="doi">10.7717/peerj-cs.20</citation>
jpayne@0:     </citations>
jpayne@0: </tool>