Mercurial > repos > iuc > plink
changeset 5:18be55ee8e08 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
| author | iuc |
|---|---|
| date | Tue, 29 Sep 2020 16:43:20 +0000 |
| parents | ac16d24f0d9d |
| children | f76d842e960f |
| files | plink.xml |
| diffstat | 1 files changed, 15 insertions(+), 14 deletions(-) [+] |
line wrap: on
line diff
--- a/plink.xml Mon Sep 28 17:00:56 2020 +0000 +++ b/plink.xml Tue Sep 29 16:43:20 2020 +0000 @@ -46,18 +46,7 @@ ## Create Plink folder for any inputs mkdir ./plink_output && mkdir ./plink_input - #if $inputs.inputs.filetype == 'bfile': - && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed - && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim - && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam - #elif $inputs.inputs.filetype == 'vcf': - #if $inputs.inputs.input.is_of_type('bcf'): - && plink --bcf '$inputs.inputs.input' - #else: - && plink --vcf '$inputs.inputs.input' - #end if - --out plink_input/plink_input - #end if + ## If bmerge is set, create folder for merged files #if $functions.func == 'data_manage': @@ -69,9 +58,21 @@ #end if #end if - ## Plink commands by section - && plink --bfile plink_input/plink_input + #if $inputs.inputs.filetype == 'bfile': + && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed + && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim + && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam + && plink --bfile plink_input/plink_input + #elif $inputs.inputs.filetype == 'vcf': + #if $inputs.inputs.input.is_of_type('bcf'): + && plink --bcf '$inputs.inputs.input' + #else: + && plink --vcf '$inputs.inputs.input' + #end if + #end if + + ## Plink commands by section #if $inputs.covar_input: --covar '$inputs.covar_input' #end if