Mercurial > repos > elixir-it > covacs_variant_recalibrator
changeset 3:733c164f2759 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Fri, 09 Nov 2018 06:52:10 -0500 |
| parents | 6863011209c4 |
| children | 91abc25944cf |
| files | tool-data/covacs_vcf.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 2 files changed, 29 insertions(+), 17 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/covacs_vcf.loc.sample Fri Nov 09 06:52:10 2018 -0500 @@ -0,0 +1,29 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory vcf file for covacs sequences data files. You will need +#to create these data files and then create a vcf_loc.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The vcf_loc.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_id> <display_name> <file_path> +# +#So, for example, if you had vcf file stored in +#/export/resource/, +#then the covacs_vcf.loc entry would look like this: +# +#hapmap hapmap /export/resource/hapmap.vcf +# +#and your /export/resource directory +#would contain hapmap.vcf. +# +# +#Your covacs_vcf.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. +# +hapmap hapmap /export/resources/hapmap.vcf +1000G 1000G /export/resources/1000G.vcf +
--- a/tool_data_table_conf.xml.sample Fri Nov 09 06:51:10 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,17 +0,0 @@ -<tables> - <!-- Location of bed-file for covacs --> - <table name="covacs_bed" comment_char="#"> - <columns> value, dbkey, name, path</columns> - <file path="tool-data/covacs_bed.loc" /> - </table> -<!-- Location of index file for covacs gatk wrapper --> - <table name="covacs_gatk_indexes" comment_char="#"> - <columns> value, dbkey, name, path</columns> - <file path="tool-data/covacs_gatk_indexes.loc" /> - </table> -<!-- Location of vcf-file for covacs VariantRecalibrator --> - <table name="covacs_vcf" comment_char="#"> - <columns> value, name, path</columns> - <file path="tool-data/covacs_vcf.loc" /> - </table> -</tables>