Mercurial > repos > iuc > gemini_load

comparison gemini_load.xml @ 4:264f4601dd1d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e4dce25c8dbeffca62c402f74ca733ddc7a6091b
author iuc
date Fri, 07 Dec 2018 12:51:01 -0500
parents 3ac6d0e85e98
children b382ddaf8445
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3:3ac6d0e85e98 4:264f4601dd1d
1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0"> 1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
2 <description>Loading a VCF file into GEMINI</description> 2 <description>Loading a VCF file into GEMINI</description>
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">load</token> 5 <token name="@BINARY@">load</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="version_command" /> 9 <expand macro="version_command" />
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 @PROVIDE_ANNO_DATA@
13
12 ln -s "${ infile }" input.vcf && 14 ln -s "${ infile }" input.vcf &&
13 bgzip -c input.vcf > input.vcf.gz && 15 bgzip -c input.vcf > input.vcf.gz &&
14 tabix -p vcf input.vcf.gz && 16 tabix -p vcf input.vcf.gz &&
15 17
16 gemini 18 gemini
17 #if $annotation_databases:
18 --annotation-dir "${annotation_databases.fields.path}"
19 #end if
20 @BINARY@ 19 @BINARY@
21 -v input.vcf.gz 20 -v input.vcf.gz
22 #if str( $annotation_type ) != "None": 21 #if str( $annotation_type ) != "None":
23 -t "$annotation_type" 22 -t "$annotation_type"
24 #end if 23 #end if