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1 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10">
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2 <description>of high-confidence SNPs, or lookup cached sitecall</description>
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3 <requirements>
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4 <requirement type="package" version="2.3.4">bowtie2</requirement>
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5 <requirement type="package" version="1.6">samtools</requirement>
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6 <requirement type="package" version="1.0.6">bzip2</requirement>
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7 <requirement type="package">picard</requirement>
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8 <requirement type="package">varscan</requirement>
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9 <requirement type="package" version="1.5.11">boto3</requirement>
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10 <requirement type="package" version="3.4">python3</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
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13 python $__tool_directory__/snp-cache.py snp_sitecalls
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14 "\$(md5sum $input $sample | cut -c -32 | md5sum | cut -c -32)"
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15 -c "
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16 cp $input ./reference.fasta &&
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17 samtools faidx ./reference.fasta &&
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18 samtools view -bS -F 4 $sample |
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19 samtools sort -o ./sorted.bam - &&
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20 picard MarkDuplicates INPUT=./sorted.bam
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21 OUTPUT=/dev/stdout
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22 METRICS_FILE=./metrics |
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23 samtools mpileup -f ./reference.fasta - -o ./pileup
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24 &&
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25 varscan mpileup2snp ./pileup
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26 --min_var-freq 0.90
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27 --output-vcf 1
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28 > ./calls
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29 && tar -zcf /dev/stdout ./metrics ./pileup ./calls
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30 "
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31 -o ./archive.tar.gz
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32 -l $cache_log
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33 && cat $cache_log
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34 && tar -zxvf ./archive.tar.gz
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35 && cp ./metrics $metrics
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36 && cp ./pileup $pileup
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37 && cp ./calls $calls
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38 ]]></command>
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39 <inputs>
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40 <param name="input" label="FASTA Reference from your history" type="data" format="fasta" />
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41 <!-- <conditional name="reads">
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42 <param name="reads_select" type="select" label="Paired-end collection, or two datasets from your history">
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43 <option value="collection">Paired collection from your history</option>
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44 <option value="history">Two FASTQ datasets from your history</option>
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45 </param>
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46 <when value="collection">
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47 <param name="coll" type="data_collection" format="fastq,fastqsanger" collection_type="paired">
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48 </when>
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49 <when value="history">
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50 <param type="data" name="forward" format="fastq,fastqsanger" />
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51 <param type="data" name="reverse" format="fastq,fastqsanger" />
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52 </when>
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53 </conditional> -->
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54 <param name="sample" label="Read alignment to reference" type="data" format="sam" />
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55 </inputs>
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56 <outputs>
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57 <data name="calls" label="${sample.name.split(' ')[0]} unfiltered SNPs" format="vcf" />
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58 <data name="pileup" label="${sample.name.split(' ')[0]} pileup" format="pileup" hidden="true" />
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59 <data name="metrics" label="Metrics from Picard" format="txt" hidden="true" />
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60 <data label="S3 Cache log" name="cache_log" format="txt" hidden="true" />
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input" value="reference/lambda_virus.fasta" />
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65 <param name="sample" value="samples/sample2/reads.sam" />
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66 <output name="calls" value="samples/sample2/var.flt.vcf" />
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67 <output name="pileup" value="samples/sample2/reads.all.pileup" />
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 <a href="http://snp-pipeline.readthedocs.io/en/latest/index.html">http://snp-pipeline.readthedocs.io/en/latest/index.html</a>
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72 ]]></help>
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73 <citations>
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74 <citation type="doi">10.7717/peerj-cs.20</citation>
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75 </citations>
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76 </tool> |
