Mercurial > repos > jpayne > snp_pipeline
comparison 2_call_sites.xml @ 0:eefdd97a6749
planemo upload commit b'7f6183b769772449fbcee903686b8d5ec5b7439f\n'-dirty
| author | jpayne |
|---|---|
| date | Wed, 24 Jan 2018 14:18:21 -0500 |
| parents | |
| children | 5191246bc2e2 |
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| -1:000000000000 | 0:eefdd97a6749 |
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| 1 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10"> | |
| 2 <description>of high-confidence SNPs, or lookup cached sitecall</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.3.4">bowtie2</requirement> | |
| 5 <requirement type="package" version="1.6">samtools</requirement> | |
| 6 <requirement type="package">picard</requirement> | |
| 7 <requirement type="package">varscan</requirement> | |
| 8 <requirement type="package" version="1.5.11">boto3</requirement> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[ | |
| 11 $__tool_directory__/snp-cache.py snp_sitecalls | |
| 12 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)" | |
| 13 -c " | |
| 14 cp $input ./reference.fasta && | |
| 15 samtools faidx ./reference.fasta && | |
| 16 samtools view -bS -F 4 $sample | | |
| 17 samtools sort -o ./sorted.bam - && | |
| 18 picard MarkDuplicates INPUT=./sorted.bam | |
| 19 OUTPUT=/dev/stdout | |
| 20 METRICS_FILE=./metrics | | |
| 21 samtools mpileup -f ./reference.fasta - -o ./pileup | |
| 22 && | |
| 23 varscan mpileup2snp ./pileup | |
| 24 --min_var-freq 0.90 | |
| 25 --output-vcf 1 | |
| 26 > ./calls | |
| 27 && tar -zcf /dev/stdout ./metrics ./pileup ./calls | |
| 28 " | |
| 29 -o ./archive.tar.gz | |
| 30 -l $cache_log | |
| 31 && cat $cache_log | |
| 32 && tar -zxvf ./archive.tar.gz | |
| 33 && cp ./metrics $metrics | |
| 34 && cp ./pileup $pileup | |
| 35 && cp ./calls $calls | |
| 36 ]]></command> | |
| 37 <inputs> | |
| 38 <param name="input" label="FASTA Reference from your history" type="data" format="fasta" /> | |
| 39 <!-- <conditional name="reads"> | |
| 40 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history"> | |
| 41 <option value="collection">Paired collection from your history</option> | |
| 42 <option value="history">Two FASTQ datasets from your history</option> | |
| 43 </param> | |
| 44 <when value="collection"> | |
| 45 <param name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired"> | |
| 46 </when> | |
| 47 <when value="history"> | |
| 48 <param type="data" name="forward" format="fastq,fastqsanger" /> | |
| 49 <param type="data" name="reverse" format="fastq,fastqsanger" /> | |
| 50 </when> | |
| 51 </conditional> --> | |
| 52 <param name="sample" label="Read alignment to reference" type="data" format="sam" /> | |
| 53 </inputs> | |
| 54 <outputs> | |
| 55 <data name="calls" label="${sample.name.split(' ')[0]} unfiltered SNPs" format="vcf" /> | |
| 56 <data name="pileup" label="${sample.name.split(' ')[0]} pileup" format="pileup" hidden="true" /> | |
| 57 <data name="metrics" label="Metrics from Picard" format="txt" hidden="true" /> | |
| 58 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" /> | |
| 59 </outputs> | |
| 60 <tests> | |
| 61 <test> | |
| 62 <param name="input" value="reference/lambda_virus.fasta" /> | |
| 63 <param name="sample" value="samples/sample2/reads.sam" /> | |
| 64 <output name="calls" value="samples/sample2/var.flt.vcf" /> | |
| 65 <output name="pileup" value="samples/sample2/reads.all.pileup" /> | |
| 66 </test> | |
| 67 </tests> | |
| 68 <help><![CDATA[ | |
| 69 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a> | |
| 70 ]]></help> | |
| 71 <citations> | |
| 72 <citation type="doi">10.7717/peerj-cs.20</citation> | |
| 73 </citations> | |
| 74 </tool> |