Mercurial > repos > iuc > bcftools_plugin_fixploidy

comparison macros.xml @ 1:ff3b5c1a6a8d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06
author iuc
date Wed, 13 Jul 2016 10:58:51 -0400
parents 7d6599c7e2fb
children b8e20c8b4caa
comparison
equal deleted inserted replaced
0:7d6599c7e2fb 1:ff3b5c1a6a8d
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@">