Mercurial > repos > devteam > vcfdistance
comparison vcfdistance.xml @ 0:6e0fc18309f4 draft
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| author | devteam |
|---|---|
| date | Thu, 19 Mar 2015 14:26:53 -0400 |
| parents | |
| children | 48e458c721b3 |
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| -1:000000000000 | 0:6e0fc18309f4 |
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| 1 <tool id="vcfdistance" name="VCFdistance:" version="0.0.3"> | |
| 2 <description>Calculate distance to the nearest variant</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"></expand> | |
| 7 <expand macro="stdio" /> | |
| 8 <command>cat "${input1}" | vcfdistance > "${out_file1}"</command> | |
| 9 <inputs> | |
| 10 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> | |
| 11 </inputs> | |
| 12 <outputs> | |
| 13 <data format="vcf" name="out_file1" /> | |
| 14 </outputs> | |
| 15 <tests> | |
| 16 <test> | |
| 17 <param name="input1" value="vcflib.vcf"/> | |
| 18 <output name="out_file1" file="vcfdistance-test1.vcf"/> | |
| 19 </test> | |
| 20 </tests> | |
| 21 <help> | |
| 22 | |
| 23 Adds a value to each VCF record indicating the distance to the nearest variant in the file. | |
| 24 | |
| 25 .. class:: infomark | |
| 26 | |
| 27 The dataset used as input to this tool must be coordinate sorted. This can be achieved by either using the VCFsort utility or Galaxy's general purpose sort tool (in this case sort on the first and the second column in ascending order). | |
| 28 | |
| 29 ---- | |
| 30 | |
| 31 Vcfdistance @IS_PART_OF_VCFLIB@ | |
| 32 </help> | |
| 33 <expand macro="citations" /> | |
| 34 </tool> |