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1 <tool id="cfsan_snp_pipeline_merge_sites" name="CFSAN SNP Pipeline: merge sites" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from multiple samples</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/snp_wind.py' ./
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9 #for $input_vcf in $input_vcf_collection:
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10 -n '$input_vcf.element_identifier' -f '$input_vcf'
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11 #end for
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12 -p 'var.fit.vcf' > ./file
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13 && cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output'
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14 ]]></command>
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15 <inputs>
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16 <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="tabular"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input_vcf_collection">
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24 <collection type="list">
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25 <element name="input1" value="input1.vcf" ftype="vcf"/>
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26 <element name="input2" value="input2.vcf" ftype="vcf"/>
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27 <element name="input3" value="input3.vcf" ftype="vcf"/>
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28 <element name="input4" value="input4.vcf" ftype="vcf"/>
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29 </collection>
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30 </param>
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31 <output name="output" value="output2.tabular"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **What it does**
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36
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37 Combine the SNP positions across all samples into a single unified SNP list
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38 file identifing the positions and sample names where SNPs were called.
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39
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40 **Optional parameters**
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41
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42 * **force** - Force processing even when result file already exists and is newer than inputs (default: False)
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43 * **vcfname** - File name of the VCF files which must exist in each of the sample directories (default: var.flt.vcf)
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44 * **maxsnps** - Exclude samples having more than this maximum allowed number of SNPs. Set to -1 to disable this function (default: -1)
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45
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46 **More information**
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47
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48 CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_
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49 ]]></help>
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50 <expand macro="citations"/>
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51 </tool>
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52
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