Mercurial > repos > iuc > gemini_load

comparison gemini_load.xml @ 2:386b3e7c2f77 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
author iuc
date Tue, 16 Feb 2016 05:54:33 -0500
parents 7f7fbd50e9dc
children 3ac6d0e85e98
comparison
equal deleted inserted replaced
1:a4e8364eb115 2:386b3e7c2f77
13 bgzip -c input.vcf > input.vcf.gz && 13 bgzip -c input.vcf > input.vcf.gz &&
14 tabix -p vcf input.vcf.gz && 14 tabix -p vcf input.vcf.gz &&
15 15
16 gemini 16 gemini
17 #if $annotation_databases: 17 #if $annotation_databases:
18 --annotation-dir ${annotation_databases.fields.path} 18 --annotation-dir "${annotation_databases.fields.path}"
19 #end if 19 #end if
20 @BINARY@ 20 @BINARY@
21 -v input.vcf.gz 21 -v input.vcf.gz
22 #if str( $annotation_type ) != "None": 22 #if str( $annotation_type ) != "None":
23 -t $annotation_type 23 -t "$annotation_type"
24 #end if 24 #end if
25 25
26 #if $ped: 26 #if $ped:
27 -p $ped 27 -p $ped
28 #end if 28 #end if
31 $skip_cadd 31 $skip_cadd
32 $skip_gene_tables 32 $skip_gene_tables
33 $no_load_genotypes 33 $no_load_genotypes
34 $no_genotypes 34 $no_genotypes
35 $passonly 35 $passonly
36 $infostring 36 "$infostring"
37 --cores \${GALAXY_SLOTS:-4} 37 --cores \${GALAXY_SLOTS:-4}
38 38
39 "${ outfile }" 39 "${ outfile }"
40 ]]> 40 ]]>
41 </command> 41 </command>