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comparison cfsan_snp_pipeline_merge_vcfs.xml @ 2:5c341fcd18ff draft default tip

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author greg
date Thu, 23 Nov 2023 19:01:14 +0000
parents ab24883161d3
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1:ab24883161d3 2:5c341fcd18ff
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.vcf' 8 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.vcf'
9 #for $input_vcf in $input_vcf_collection 9 #for $input_vcf in $input_vcf_collection
10 -n '$input_vcf.element_identifier' -f '$input_vcf' 10 -n '$input_vcf.element_identifier' -f '$input_vcf'
11 #end for 11 #end for
12 > ./file 12 > ./file &&
13 && cfsan_snp_pipeline merge_vcfs ./file 13 cfsan_snp_pipeline merge_vcfs ./file &&
14 mv snpma.vcf '$output'
14 ]]></command> 15 ]]></command>
15 <inputs> 16 <inputs>
16 <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/> 17 <param name="input_vcf_collection" type="data_collection" format="vcf" collection_type="list" label="Collection of VCF files"/>
17 </inputs> 18 </inputs>
18 <outputs> 19 <outputs>
19 <data name="output" format="vcf"/> 20 <data name="output" label="SNP matrix" format="vcf"/>
20 </outputs> 21 </outputs>
21 <tests> 22 <tests>
22 <test> 23 <test>
23 <param name="input_vcf_collection"> 24 <param name="input_vcf_collection">
24 <collection type="list"> 25 <collection type="list">
28 <element name="sample4" value="samples/sample4/consensus.vcf" ftype="vcf"/> 29 <element name="sample4" value="samples/sample4/consensus.vcf" ftype="vcf"/>
29 </collection> 30 </collection>
30 </param> 31 </param>
31 <output name="output" ftype="vcf"> 32 <output name="output" ftype="vcf">
32 <assert_contents> 33 <assert_contents>
33 <has_size value="0" delta="100"/> 34 <has_size value="31888" delta="100"/>
34 </assert_contents> 35 </assert_contents>
35 </output> 36 </output>
36 </test> 37 </test>
37 </tests> 38 </tests>
38 <help><![CDATA[ 39 <help><![CDATA[