Mercurial > repos > greg > vsnp_get_snps

comparison vsnp_get_snps.xml @ 13:cd636b0e4f95 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_get_snps commit cab8ee43e902a3ae7b0fd6b06842c4b5c221af25"
author greg
date Tue, 21 Sep 2021 00:21:36 +0000
parents 544b2ed99a9a
children 44b84d32883c
comparison
equal deleted inserted replaced
12:544b2ed99a9a 13:cd636b0e4f95
26 #set dbkey = '?' 26 #set dbkey = '?'
27 #for $i in $input_additional_zc_vcf_collection_cond.input_vcf_collection: 27 #for $i in $input_additional_zc_vcf_collection_cond.input_vcf_collection:
28 #if str($dbkey) == '?': 28 #if str($dbkey) == '?':
29 #set dbkey = $i.metadata.dbkey 29 #set dbkey = $i.metadata.dbkey
30 #else if str($dbkey) != $i.metadata.dbkey: 30 #else if str($dbkey) != $i.metadata.dbkey:
31 >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique" && exit 1 31 >&2 echo "The dbkeys associated with the zero coverage VCF files with SNPs found in closely related isolate groups are not unique, check ${i.name}" && exit 1
32 #end if 32 #end if
33 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) 33 #set vcf_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
34 ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' && 34 ln -s '${i}' '$input_vcf_dir/${vcf_identifier}' &&
35 #end for 35 #end for
36 #if str($dbkey) == '?': 36 #if str($dbkey) == '?':