Mercurial > repos > iuc > plink
comparison plink.xml @ 4:ac16d24f0d9d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 577ea693a59004c6fa892d079cd0b2b835ee59bf"
| author | iuc |
|---|---|
| date | Mon, 28 Sep 2020 17:00:56 +0000 |
| parents | 57ac42ec1be3 |
| children | 18be55ee8e08 |
comparison
equal
deleted
inserted
replaced
| 3:57ac42ec1be3 | 4:ac16d24f0d9d |
|---|---|
| 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> |