Mercurial > repos > iuc > bcftools_convert_to_vcf
comparison macros.xml @ 6:1f2183a23823 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3
| author | iuc |
|---|---|
| date | Tue, 12 Dec 2017 14:02:26 -0500 |
| parents | 7b50ab23976c |
| children | 367ba501b6eb |
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| 5:7b50ab23976c | 6:1f2183a23823 |
|---|---|
| 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 |