Mercurial > repos > elixir-it > covacs_tabix

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