Mercurial > repos > iuc > bcftools_merge
comparison macros.xml @ 6:85ee7e6c4204 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3
author | iuc |
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date | Tue, 12 Dec 2017 13:56:42 -0500 |
parents | c5c61f2f8757 |
children | 7ba36babba2d |
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5:c5c61f2f8757 | 6:85ee7e6c4204 |
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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 |