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1 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
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2 <description>from multiple samples</description>
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3 <requirements>
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4 <container type="docker">quay.io/staphb/cfsan-snp-pipeline</container>
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5 <!-- <requirement type="package" version="2.4.5">bowtie2</requirement>
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6 <requirement type="package" version="1.9">samtools</requirement>
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7 <requirement type="package" version="1.0.8">bzip2</requirement>
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8 <requirement type="package" version="2.2.1">snp-pipeline</requirement> -->
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9 <!-- <requirement type="package" version="3.6.8">python</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 python $__tool_directory__/snp-wind.py ./
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14 #for $call in $calls
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15 -n $call.element_identifier -f $call
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16 #end for
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17 -p "var.fit.vcf" > ./file
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18 && cfsan_snp_pipeline merge_sites -v 4 -n "var.fit.vcf" ./file ./filtered_snps -o $snplist
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19 ]]></command>
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20 <inputs>
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21 <param type="data_collection" name="calls" format="vcf" collection_type="list" />
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22 </inputs>
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23 <outputs>
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24 <data name="snplist" format="txt" />
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="calls">
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29 <collection type="list">
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30 <element name="sample1" value="samples/sample1/var.flt_preserved.vcf" ftype="fastqsanger" />
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31 <element name="sample2" value="samples/sample2/var.flt_preserved.vcf" ftype="fastqsanger" />
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32 <element name="sample3" value="samples/sample3/var.flt_preserved.vcf" ftype="fastqsanger" />
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33 <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" />
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34 </collection>
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35 </param>
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36 <output name="snplist" value="snplist.txt" />
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 <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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41 ]]></help>
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42 <citations>
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43 <citation type="doi">10.7717/peerj-cs.20</citation>
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44 </citations>
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45 </tool> |
