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comparison plink.xml @ 5:a3ab534043ff draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit d27eb518580d91d21b7004e6e6b48079eea5ff9b"
author iuc
date Tue, 29 Sep 2020 16:42:38 +0000
parents 2d1b7d7b32a9
children 111c1d98d670
comparison
equal deleted inserted replaced
4:2d1b7d7b32a9 5:a3ab534043ff
44 <command detect_errors='exit_code'><![CDATA[ 44 <command detect_errors='exit_code'><![CDATA[
45 45
46 ## Create Plink folder for any inputs 46 ## Create Plink folder for any inputs
47 mkdir ./plink_output 47 mkdir ./plink_output
48 && mkdir ./plink_input 48 && mkdir ./plink_input
49 #if $inputs.inputs.filetype == 'bfile': 49
50 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
51 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
52 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
53 #elif $inputs.inputs.filetype == 'vcf':
54 #if $inputs.inputs.input.is_of_type('bcf'):
55 && plink --bcf '$inputs.inputs.input'
56 #else:
57 && plink --vcf '$inputs.inputs.input'
58 #end if
59 --out plink_input/plink_input
60 #end if
61 50
62 ## If bmerge is set, create folder for merged files 51 ## If bmerge is set, create folder for merged files
63 #if $functions.func == 'data_manage': 52 #if $functions.func == 'data_manage':
64 #if $functions.bmerge.set == 'Yes': 53 #if $functions.bmerge.set == 'Yes':
65 && mkdir bmerge_files 54 && mkdir bmerge_files
67 && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim 56 && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim
68 && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam 57 && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam
69 #end if 58 #end if
70 #end if 59 #end if
71 60
61
62 #if $inputs.inputs.filetype == 'bfile':
63 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
64 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
65 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
66 && plink --bfile plink_input/plink_input
67 #elif $inputs.inputs.filetype == 'vcf':
68 #if $inputs.inputs.input.is_of_type('bcf'):
69 && plink --bcf '$inputs.inputs.input'
70 #else:
71 && plink --vcf '$inputs.inputs.input'
72 #end if
73 #end if
74
72 ## Plink commands by section 75 ## Plink commands by section
73
74 && plink --bfile plink_input/plink_input
75 #if $inputs.covar_input: 76 #if $inputs.covar_input:
76 --covar '$inputs.covar_input' 77 --covar '$inputs.covar_input'
77 #end if 78 #end if
78 #if $inputs.pheno: 79 #if $inputs.pheno:
79 --pheno $inputs.pheno 80 --pheno $inputs.pheno