Mercurial > repos > elixir-it > covacs_tabix
comparison covacs_tabix.xml @ 0:a408f7737cf0 draft default tip
Uploaded
| author | elixir-it |
|---|---|
| date | Thu, 08 Nov 2018 12:57:58 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:a408f7737cf0 |
|---|---|
| 1 <tool id="covacs_tabix" name="covacs_tabix" version="0.2.6"> | |
| 2 <description> tabix wrapper for covacs </description> | |
| 3 <macros> | |
| 4 </macros> | |
| 5 <requirements> | |
| 6 <requirement type="package" version="0.2.6" >tabix</requirement> | |
| 7 </requirements> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 | |
| 11 ln -s $input1 covacs.vcf && | |
| 12 | |
| 13 bgzip covacs.vcf && | |
| 14 tabix covacs.vcf.gz | |
| 15 | |
| 16 ]]> | |
| 17 </command> | |
| 18 <inputs> | |
| 19 <param format="vcf" name="input1" label="input vcf " type="data" optional="true" /> | |
| 20 </inputs> | |
| 21 <outputs> | |
| 22 <data format="bgzip" name="bgzip_output" from_work_dir="covacs.vcf.gz" label="bgzip on ${on_string}"/> | |
| 23 <data format="tabix" name="tabix_output" from_work_dir="covacs.vcf.gz.tbi" label="tabix on ${on_string}"/> | |
| 24 </outputs> | |
| 25 <help> | |
| 26 The final output of the wrapper consists of two files | |
| 27 | |
| 28 - file.vcf.gz from bgzip | |
| 29 - file.vcf.gz.tbi from tabix | |
| 30 | |
| 31 **more informations** at http://www.htslib.org/doc/tabix.html | |
| 32 </help> | |
| 33 <citations> | |
| 34 <citation type="doi">10.1186/s12864-018-4508-1</citation> | |
| 35 <citation type="doi">10.1093/bioinformatics/btq671</citation> | |
| 36 </citations> | |
| 37 </tool> | |
| 38 |