Mercurial > repos > anton > vcfdistance
annotate vcfdistance.xml @ 3:49482c68e701 draft default tip
Uploaded
| author | anton |
|---|---|
| date | Mon, 15 Sep 2014 14:50:50 -0400 |
| parents | 2c664ebd4af5 |
| children |
| rev | line source |
|---|---|
|
2
2c664ebd4af5
Updated tool version to 0.0.2
Anton Nekrutenko <anton@bx.psu.edu>
parents:
1
diff
changeset
|
1 <tool id="vcfdistance" name="VCFdistance:" version="0.0.2"> |
| 0 | 2 <requirements> |
| 3 | 3 <requirement type="package" version="8a5602bf07">vcflib</requirement> |
| 0 | 4 </requirements> |
| 5 <description>Calculate distance to the nearest variant</description> | |
| 6 <command>cat "${input1}" | vcfdistance > "${out_file1}"</command> | |
| 7 <inputs> | |
| 3 | 8 <param format="vcf" name="input1" type="data" label="Select VCF dataset"/> |
| 0 | 9 </inputs> |
| 10 <outputs> | |
| 11 <data format="vcf" name="out_file1" /> | |
| 12 </outputs> | |
| 13 <tests> | |
| 14 <test> | |
| 15 <param name="input1" value="vcflib.vcf"/> | |
| 16 <output name="out_file1" file="vcfdistance-test1.vcf"/> | |
| 17 </test> | |
| 18 </tests> | |
| 19 <help> | |
| 20 | |
| 21 Adds a value to each VCF record indicating the distance to the nearest variant in the file. | |
| 22 | |
| 23 .. class:: infomark | |
| 24 | |
| 25 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). | |
| 26 | |
| 27 ---- | |
| 28 | |
| 29 Vcfdistance is a part of VCFlib toolkit developed by Erik Garrison (https://github.com/ekg/vcflib). | |
| 30 | |
| 31 </help> | |
| 32 </tool> |