Mercurial > repos > iuc > bcftools_gtcheck

comparison macros.xml @ 6:501bfb078342 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3
author iuc
date Tue, 12 Dec 2017 13:58:59 -0500
parents 9d243d49870f
children a1213a0b7b66
comparison
equal deleted inserted replaced
5:9d243d49870f 6:501bfb078342
47 #set $input_vcf = 'input.vcf.gz' 47 #set $input_vcf = 'input.vcf.gz'
48 #if $input_file.is_of_type('vcf') 48 #if $input_file.is_of_type('vcf')
49 bgzip -c '$input_file' > $input_vcf && 49 bgzip -c '$input_file' > $input_vcf &&
50 bcftools index $input_vcf && 50 bcftools index $input_vcf &&
51 #elif $input_file.is_of_type('vcf_bgzip') 51 #elif $input_file.is_of_type('vcf_bgzip')
52 ln -s '$input_file' $input_vcf 52 ln -s '$input_file' $input_vcf &&
53 #elif $input_file.is_of_type('bcf') 53 #elif $input_file.is_of_type('bcf')
54 #set $input_vcf = 'input.bcf' 54 #set $input_vcf = 'input.bcf'
55 ln -s '$input_file' $input_vcf && 55 ln -s '$input_file' $input_vcf &&
56 #if $input_file.metadata.bcf_index: 56 #if $input_file.metadata.bcf_index:
57 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi && 57 ln -s '${input_file.metadata.bcf_index}' ${input_vcf}.csi &&
58 #else 58 #else
59 bcftools index $input_vcf && 59 bcftools index $input_vcf &&
60 #end if 60 #end if
61 #elif $input_file.is_of_type('bcf_bgzip') 61 #elif $input_file.is_of_type('bcf_bgzip')
62 ln -s '$input_file' $input_vcf 62 ln -s '$input_file' $input_vcf &&
63 #end if 63 #end if
64 ]]> 64 ]]>
65 </token> 65 </token>
66 <token name="@INPUT_FILE@"> 66 <token name="@INPUT_FILE@">
67 $input_vcf 67 $input_vcf