Mercurial > repos > iuc > bcftools_convert_to_vcf
comparison macros.xml @ 1:b8926b599d45 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06
| author | iuc |
|---|---|
| date | Wed, 13 Jul 2016 10:56:52 -0400 |
| parents | b068ef999550 |
| children | 98d4a7bfec83 |
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| 0:b068ef999550 | 1:b8926b599d45 |
|---|---|
| 75 ## May need to symlink input if there is an associated | 75 ## May need to symlink input if there is an associated |
| 76 #set $input_vcfs = [] | 76 #set $input_vcfs = [] |
| 77 #set $vcfs_list_file = 'vcfs_list' | 77 #set $vcfs_list_file = 'vcfs_list' |
| 78 #for (i,input_file) in enumerate($input_files): | 78 #for (i,input_file) in enumerate($input_files): |
| 79 #set $input_vcf = 'input' + str($i) + '.vcf.gz' | 79 #set $input_vcf = 'input' + str($i) + '.vcf.gz' |
| 80 echo '$input_vcf' >> $vcfs_list_file && | |
| 81 #if $input_file.datatype.file_ext == 'vcf' | 80 #if $input_file.datatype.file_ext == 'vcf' |
| 82 bgzip -c "$input_file" > $input_vcf && | 81 bgzip -c "$input_file" > $input_vcf && |
| 83 bcftools index $input_vcf && | 82 bcftools index $input_vcf && |
| 84 #elif $input_file.datatype.file_ext == 'vcf_bgz' | 83 #elif $input_file.datatype.file_ext == 'vcf_bgz' |
| 85 ln -s "$input_file" $input_vcf | 84 ln -s "$input_file" $input_vcf |
| 93 bcftools index $input_vcf && | 92 bcftools index $input_vcf && |
| 94 #end if | 93 #end if |
| 95 #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' | 94 #elif $input_file.datatype.file_ext == 'bcfvcf_bgz' |
| 96 ln -s "$input_file" $input_vcf && | 95 ln -s "$input_file" $input_vcf && |
| 97 #end if | 96 #end if |
| 97 echo '$input_vcf' >> $vcfs_list_file && | |
| 98 $input_vcfs.append($input_vcf) | 98 $input_vcfs.append($input_vcf) |
| 99 #end for | 99 #end for |
| 100 ]]> | 100 ]]> |
| 101 </token> | 101 </token> |
| 102 <token name="@INPUT_FILES@"> | 102 <token name="@INPUT_FILES@"> |