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comparison plink.xml @ 4:2d1b7d7b32a9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 577ea693a59004c6fa892d079cd0b2b835ee59bf"
author iuc
date Mon, 28 Sep 2020 17:00:13 +0000
parents d6442267be14
children a3ab534043ff
comparison
equal deleted inserted replaced
3:d6442267be14 4:2d1b7d7b32a9
49 #if $inputs.inputs.filetype == 'bfile': 49 #if $inputs.inputs.filetype == 'bfile':
50 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed 50 && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed
51 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim 51 && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim
52 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam 52 && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam
53 #elif $inputs.inputs.filetype == 'vcf': 53 #elif $inputs.inputs.filetype == 'vcf':
54 #if $inputs.inputs.input.is_of_type('vcf'): 54 #if $inputs.inputs.input.is_of_type('bcf'):
55 && plink --bcf '$inputs.inputs.input'
56 #else:
55 && plink --vcf '$inputs.inputs.input' 57 && plink --vcf '$inputs.inputs.input'
56 #else:
57 && plink --bcf '$inputs.inputs.input'
58 #end if 58 #end if
59 --out plink_input/plink_input 59 --out plink_input/plink_input
60 #end if 60 #end if
61 61
62 ## If bmerge is set, create folder for merged files 62 ## If bmerge is set, create folder for merged files
392 <param format='pbed' name='bed' type='data' label='plink bed file'/> 392 <param format='pbed' name='bed' type='data' label='plink bed file'/>
393 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> 393 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
394 <param format='txt' name='fam' type='data' label='plink fam file'/> 394 <param format='txt' name='fam' type='data' label='plink fam file'/>
395 </when> 395 </when>
396 <when value='vcf'> 396 <when value='vcf'>
397 <param name='input' format='vcf,bcf' type='data' label='VCF/BCF Input file'/> 397 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
398 </when> 398 </when>
399 </conditional> 399 </conditional>
400 <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/> 400 <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/>
401 <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/> 401 <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/>
402 </section> 402 </section>