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1 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
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2 <description>into a multi-sample VCF with consensus SNPs</description>
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3 <requirements>
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4 <requirement type="package" version="1.6">bcftools</requirement>
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5 <requirement type="package" version="1.0.6">bzip2</requirement>
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6 <requirement type="package" version="1.0.1">snp-pipeline</requirement>
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7 <requirement type="package" version="0.2.5">tabix</requirement>
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8 <!-- <requirement type="package" version="3.5">python</requirement> -->
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9 <requirement type="package" version="1.6">htslib</requirement>
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10 </requirements>
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11 <command detect_errors="exit_code"><![CDATA[
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12 export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
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13 env &&
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14 ls -lah \$CONDA_DEFAULT_ENV/bin &&
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15 ls -lah \$CONDA_DEFAULT_ENV/lib &&
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16 python $__tool_directory__/snp-wind.py ./ -p "consensus.vcf"
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17 #for $vcf in $vcfs
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18 -n $vcf.element_identifier -f $vcf
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19 #end for
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20 > ./file
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21 && cat ./file
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22 && cfsan_snp_pipeline merge_vcfs ./file
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23 ]]></command>
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24 <inputs>
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25 <param type="data_collection" format="vcf" collection_type="list" name="vcfs" label="List of VCFs" />
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26 </inputs>
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27 <outputs>
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28 <data format="vcf" label="SNP matrix" name="snpmav" from_work_dir="snpma.vcf"/>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="vcfs">
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33 <collection type="list">
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34 <element name="sample1" value="samples/sample1/consensus.vcf" />
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35 <element name="sample2" value="samples/sample2/consensus.vcf" />
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36 <element name="sample3" value="samples/sample3/consensus.vcf" />
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37 <element name="sample4" value="samples/sample4/consensus.vcf" />
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38 </collection>
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39 </param>
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40 <output name="snpmav" value="snpma.vcf" lines_diff="2" />
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 <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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45 ]]></help>
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46 <citations>
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47 <citation type="doi">10.7717/peerj-cs.20</citation>
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48 </citations>
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49 </tool> |
