jpayne@0: <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10">
jpayne@0:     <description>of high-confidence SNPs, or lookup cached sitecall</description>
jpayne@0:     <requirements>
jpayne@0:         <requirement type="package" version="2.3.4">bowtie2</requirement>
jpayne@0:         <requirement type="package" version="1.6">samtools</requirement>
jpayne@5:         <requirement type="package" version="1.0.6">bzip2</requirement>
jpayne@0:         <requirement type="package">picard</requirement>
jpayne@0:         <requirement type="package">varscan</requirement>
jpayne@0:         <requirement type="package" version="1.5.11">boto3</requirement>
jpayne@37:         <!-- <requirement type="package" version="3.5">python</requirement> -->
jpayne@0:     </requirements>
jpayne@0:     <command detect_errors="exit_code"><![CDATA[
jpayne@9:     python $__tool_directory__/snp-cache.py snp_sitecalls 
jpayne@0:         "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
jpayne@0:         -c "
jpayne@0:             cp $input ./reference.fasta                    &&
jpayne@0:             samtools faidx ./reference.fasta               &&  
jpayne@0:             samtools view -bS -F 4 $sample |
jpayne@0:             samtools sort -o ./sorted.bam -                &&
jpayne@0:             picard MarkDuplicates INPUT=./sorted.bam
jpayne@0:                                   OUTPUT=/dev/stdout 
jpayne@0:                                   METRICS_FILE=./metrics |
jpayne@0:             samtools mpileup -f ./reference.fasta - -o ./pileup
jpayne@0:             &&
jpayne@0:             varscan mpileup2snp ./pileup
jpayne@0:                                 --min_var-freq 0.90 
jpayne@0:                                 --output-vcf 1
jpayne@0:             > ./calls
jpayne@0:             && tar -zcf /dev/stdout ./metrics ./pileup ./calls
jpayne@0:         "
jpayne@0:         -o ./archive.tar.gz
jpayne@0:         -l $cache_log
jpayne@0:         && cat $cache_log
jpayne@0:         && tar -zxvf ./archive.tar.gz
jpayne@0:         && cp ./metrics $metrics
jpayne@0:         && cp ./pileup $pileup
jpayne@0:         && cp ./calls $calls
jpayne@0:     ]]></command>
jpayne@0:     <inputs>
jpayne@0:         <param name="input" label="FASTA Reference from your history" type="data" format="fasta" />
jpayne@0:         <!-- <conditional name="reads">
jpayne@0:             <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
jpayne@0:                 <option value="collection">Paired collection from your history</option>
jpayne@0:                 <option value="history">Two FASTQ datasets from your history</option>
jpayne@0:             </param>
jpayne@0:             <when value="collection">
jpayne@0:                 <param name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired">
jpayne@0:             </when>
jpayne@0:             <when value="history">
jpayne@0:                 <param type="data" name="forward" format="fastq,fastqsanger" />
jpayne@0:                 <param type="data" name="reverse" format="fastq,fastqsanger" />
jpayne@0:             </when>
jpayne@0:         </conditional> -->
jpayne@0:         <param name="sample" label="Read alignment to reference" type="data" format="sam" />
jpayne@0:     </inputs>
jpayne@0:     <outputs>
jpayne@0:         <data name="calls" label="${sample.name.split(' ')[0]} unfiltered SNPs" format="vcf" />
jpayne@0:         <data name="pileup" label="${sample.name.split(' ')[0]} pileup" format="pileup" hidden="true" />
jpayne@0:         <data name="metrics" label="Metrics from Picard" format="txt" 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="input" value="reference/lambda_virus.fasta" />
jpayne@0:             <param name="sample" value="samples/sample2/reads.sam" />
jpayne@0:             <output name="calls" value="samples/sample2/var.flt.vcf" />
jpayne@0:             <output name="pileup" value="samples/sample2/reads.all.pileup" />
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>