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1 <tool id="cfsan_snp_pipeline_merge_vcfs" name="CFSAN SNP Pipeline: merge vcfs" 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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1
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8 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.vcf'
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9 #for $input_vcf in $input_vcf_collection
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10 -n '$input_vcf.element_identifier' -f '$input_vcf'
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11 #end for
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12 > ./file &&
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13 cfsan_snp_pipeline merge_vcfs ./file &&
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14 mv snpma.vcf '$output'
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15 ]]></command>
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16 <inputs>
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17 <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
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18 </inputs>
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19 <outputs>
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2
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20 <data name="output" label="SNP matrix" format="vcf"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input_vcf_collection">
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25 <collection type="list">
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26 <element name="sample1" value="samples/sample1/consensus.vcf" ftype="vcf"/>
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27 <element name="sample2" value="samples/sample2/consensus.vcf" ftype="vcf"/>
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28 <element name="sample3" value="samples/sample3/consensus.vcf" ftype="vcf"/>
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29 <element name="sample4" value="samples/sample4/consensus.vcf" ftype="vcf"/>
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30 </collection>
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31 </param>
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32 <output name="output" ftype="vcf">
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33 <assert_contents>
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34 <has_size value="31888" delta="100"/>
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 **What it does**
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41
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42 Merges the consensus vcf files from all samples into a single multi-vcf file.
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43
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44 **More information**
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45
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46 CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_
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47 ]]></help>
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48 <expand macro="citations"/>
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49 </tool>
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50
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