Mercurial > repos > iuc > plink
changeset 7:66b35562554d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27"
| author | iuc |
|---|---|
| date | Mon, 05 Oct 2020 16:08:24 +0000 |
| parents | f76d842e960f |
| children | 16d22eee0fe3 |
| files | plink.xml |
| diffstat | 1 files changed, 59 insertions(+), 56 deletions(-) [+] |
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line diff
--- a/plink.xml Wed Sep 30 20:29:06 2020 +0000 +++ b/plink.xml Mon Oct 05 16:08:24 2020 +0000 @@ -1,7 +1,7 @@ <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> <macros> <token name='@TOOL_VERSION@'>1.9.b618</token> - <token name='@VERSION_SUFFIX@'>1</token> + <token name='@VERSION_SUFFIX@'>2</token> <xml name='template_sanitizer'> <sanitizer> <valid initial='default'> @@ -76,8 +76,8 @@ #if $inputs.covar_input: --covar '$inputs.covar_input' #end if - #if $inputs.pheno: - --pheno $inputs.pheno + #if $inputs.set_pheno.set_pheno == 'Yes': + --pheno $inputs.set_pheno.pheno $inputs.set_pheno.all_pheno #end if #if $functions.func == 'filtering': ##ID list functions @@ -381,6 +381,24 @@ --memory \${GALAXY_MEMORY_MB:-8192} --make-bed --out plink_output/plink_output + + #if $functions.func == 'association': + #if $functions.logistic.logistic == 'Yes': + && mkdir logistic_out + && mv plink_output/plink_output.*.l* logistic_out + && find ./logistic_out/. -type f -exec mv {} {}.txt ';' + #end if + #if $functions.adjust.adjust == 'Yes': + && mkdir adjust_out + && mv ./plink_output/*.adjuste* adjust_out + && find ./adjust_out/. -type f -exec mv {} {}.txt ';' + #end if + #if $functions.assoc.assoc == 'Yes': + && mkdir assoc_out + && mv ./plink_output/*asso* assoc_out + && find ./assoc_out/. -type f -exec mv {} {}.txt ';' + #end if + #end if ]]></command> <inputs> <section name='inputs' title='Data inputs' expanded='true'> @@ -398,7 +416,17 @@ <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/> </when> </conditional> - <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/> + <conditional name='set_pheno'> + <param name='set_pheno' type='select' label='Set phenotype'> + <option value=''>No</option> + <option value='Yes'>Yes</option> + </param> + <when value=''/> + <when value='Yes'> + <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.'/> + <param name='all_pheno' type='boolean' truevalue='--all-pheno' falsevalue='' label='Allow all phenotypes present in the phenotype file to be subject to the association tests you have requested' checked='false'/> + </when> + </conditional> <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/> </section> <conditional name='functions'> @@ -998,52 +1026,21 @@ </data> <!--Association--> - <!--assoc--> - <data name='assoc' format='tabular' from_work_dir='plink_output/plink_output.assoc' label='${tool.name}: Association'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and not functions['assoc']['fisher']</filter> - </data> - <data name='perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.perm' label='${tool.name}: Association Monte Carlo'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and not functions['assoc']['fisher']</filter> - </data> - <data name='mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.mperm' label='${tool.name}: Association Max(T) permutation test'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and not functions['assoc']['fisher']</filter> - </data> - <data name='fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher' label='${tool.name}: Association Fisher'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['fisher']</filter> - </data> - <data name='fisher_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.perm' label='${tool.name}: Association Fisher perm'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and functions['assoc']['fisher']</filter> - </data> - <data name='fisher_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.mperm' label='${tool.name}: Association Fisher mperm'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and functions['assoc']['fisher']</filter> - </data> - - <!--adjust--> - <data name='adjust' format='tabular' from_work_dir='plink_output/plink_output.assoc.adjusted' label='${tool.name}: Adjusted'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and not functions['assoc']['fisher']</filter> - </data> - <data name='adjust_fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.adjusted' label='${tool.name}: Fisher Adjusted'> - <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and functions['assoc']['fisher']</filter> - </data> - <data name='adjust_logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.adjusted' label='${tool.name}: Logistic Adjusted'> - <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes' and functions['logistic']['logistic'] == 'Yes'</filter> - </data> - - <!-- <data name='linear' format='tabular' from_work_dir='plink_output/plink_output.assoc.linenar' label='${tool.name}: Linear Regression'> - <filter>functions['func'] == 'association' and functions.func.association.linear['linear'] == 'Yes'</filter> - </data> --> - + <!--Assoc --> + <collection name='assoc_outfiles' type='list' label='Association outfiles'> + <discover_datasets directory='assoc_out' pattern='__name_and_ext__'/> + <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes'</filter> + </collection> + <!--Adjust--> + <collection name='adjust_outfiles' type='list' label='Adjust outfiles'> + <discover_datasets directory='adjust_out' pattern='__name_and_ext__'/> + <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes'</filter> + </collection> <!--Logistic--> - <data name='logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic' label='${tool.name}: Logistic Regression'> - <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter> - </data> - <data name='logistic_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.perm' label='${tool.name}: Logistic Association Monte Carlo'> - <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'perm'</filter> - </data> - <data name='logistic_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.mperm' label='${tool.name}: Logistic Association Max(T) permutation test'> - <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'mperm'</filter> - </data> - + <collection name='log_outfiles' type='list' label='Logistic outfiles'> + <discover_datasets directory='logistic_out' pattern='__name_and_ext__'/> + <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter> + </collection> <!--Link--> <data name='prune_in' format='tabular' from_work_dir='plink_output/plink_output.prune.in' label='${tool.name}: Prune In'> <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter> @@ -1291,7 +1288,7 @@ <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/> </test> - <test expect_num_outputs='11'> + <test expect_num_outputs='8'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> @@ -1333,12 +1330,18 @@ <element name='plink_bim' file='out.assoc.bim'/> <element name='plink_fam' file='out.assoc.fam'/> </output_collection> - <output name='fisher' value="out.assoc.fisher"/> - <output name='adjust_fisher' value="out.assoc.fisher.adjusted" sort="True" /> - <output name='fisher_mperm' value="out.assoc.fisher.mperm" compare='sim_size'/> - <output name='logistic' value="out.assoc.logistic"/> - <output name='adjust_logistic' value="out.assoc.logistic.adjusted"/> - <output name='logistic_perm' value="out.assoc.logistic.perm" compare='sim_size'/> + <output_collection name='assoc_outfiles' type='list' count='2'> + <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/> + <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/> + </output_collection> + <output_collection name='adjust_outfiles' type='list' count='1'> + <element name='plink_output.assoc.fisher.adjusted' value='out.assoc.fisher.adjusted' compare='sim_size' /> + </output_collection> + <output_collection name='log_outfiles' type='list' count='3'> + <element name='plink_output.assoc.logistic' value='out.assoc.logistic'/> + <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/> + <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/> + </output_collection> </test> <test expect_num_outputs='6'>