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comparison plink.xml @ 7:66b35562554d draft

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"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
comparison
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6:f76d842e960f 7:66b35562554d
1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> 1 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
2 <macros> 2 <macros>
3 <token name='@TOOL_VERSION@'>1.9.b618</token> 3 <token name='@TOOL_VERSION@'>1.9.b618</token>
4 <token name='@VERSION_SUFFIX@'>1</token> 4 <token name='@VERSION_SUFFIX@'>2</token>
5 <xml name='template_sanitizer'> 5 <xml name='template_sanitizer'>
6 <sanitizer> 6 <sanitizer>
7 <valid initial='default'> 7 <valid initial='default'>
8 <add value='#' /> 8 <add value='#' />
9 <add value='@' /> 9 <add value='@' />
74 74
75 ## Plink commands by section 75 ## Plink commands by section
76 #if $inputs.covar_input: 76 #if $inputs.covar_input:
77 --covar '$inputs.covar_input' 77 --covar '$inputs.covar_input'
78 #end if 78 #end if
79 #if $inputs.pheno: 79 #if $inputs.set_pheno.set_pheno == 'Yes':
80 --pheno $inputs.pheno 80 --pheno $inputs.set_pheno.pheno $inputs.set_pheno.all_pheno
81 #end if 81 #end if
82 #if $functions.func == 'filtering': 82 #if $functions.func == 'filtering':
83 ##ID list functions 83 ##ID list functions
84 #if $functions.id_list.func == 'keep': 84 #if $functions.id_list.func == 'keep':
85 --keep '$functions.id_list.file' 85 --keep '$functions.id_list.file'
379 ## 379 ##
380 #end if 380 #end if
381 --memory \${GALAXY_MEMORY_MB:-8192} 381 --memory \${GALAXY_MEMORY_MB:-8192}
382 --make-bed 382 --make-bed
383 --out plink_output/plink_output 383 --out plink_output/plink_output
384
385 #if $functions.func == 'association':
386 #if $functions.logistic.logistic == 'Yes':
387 && mkdir logistic_out
388 && mv plink_output/plink_output.*.l* logistic_out
389 && find ./logistic_out/. -type f -exec mv {} {}.txt ';'
390 #end if
391 #if $functions.adjust.adjust == 'Yes':
392 && mkdir adjust_out
393 && mv ./plink_output/*.adjuste* adjust_out
394 && find ./adjust_out/. -type f -exec mv {} {}.txt ';'
395 #end if
396 #if $functions.assoc.assoc == 'Yes':
397 && mkdir assoc_out
398 && mv ./plink_output/*asso* assoc_out
399 && find ./assoc_out/. -type f -exec mv {} {}.txt ';'
400 #end if
401 #end if
384 ]]></command> 402 ]]></command>
385 <inputs> 403 <inputs>
386 <section name='inputs' title='Data inputs' expanded='true'> 404 <section name='inputs' title='Data inputs' expanded='true'>
387 <conditional name='inputs'> 405 <conditional name='inputs'>
388 <param name='filetype' type='select' label='Main input data type'> 406 <param name='filetype' type='select' label='Main input data type'>
396 </when> 414 </when>
397 <when value='vcf'> 415 <when value='vcf'>
398 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/> 416 <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>
399 </when> 417 </when>
400 </conditional> 418 </conditional>
401 <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'/> 419 <conditional name='set_pheno'>
420 <param name='set_pheno' type='select' label='Set phenotype'>
421 <option value=''>No</option>
422 <option value='Yes'>Yes</option>
423 </param>
424 <when value=''/>
425 <when value='Yes'>
426 <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.'/>
427 <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'/>
428 </when>
429 </conditional>
402 <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/> 430 <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/>
403 </section> 431 </section>
404 <conditional name='functions'> 432 <conditional name='functions'>
405 <param name='func' type='select' label='Plink functions'> 433 <param name='func' type='select' label='Plink functions'>
406 <option value='filtering'>Filtering</option> 434 <option value='filtering'>Filtering</option>
996 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'> 1024 <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'>
997 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter> 1025 <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter>
998 </data> 1026 </data>
999 1027
1000 <!--Association--> 1028 <!--Association-->
1001 <!--assoc--> 1029 <!--Assoc -->
1002 <data name='assoc' format='tabular' from_work_dir='plink_output/plink_output.assoc' label='${tool.name}: Association'> 1030 <collection name='assoc_outfiles' type='list' label='Association outfiles'>
1003 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and not functions['assoc']['fisher']</filter> 1031 <discover_datasets directory='assoc_out' pattern='__name_and_ext__'/>
1004 </data> 1032 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes'</filter>
1005 <data name='perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.perm' label='${tool.name}: Association Monte Carlo'> 1033 </collection>
1006 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and not functions['assoc']['fisher']</filter> 1034 <!--Adjust-->
1007 </data> 1035 <collection name='adjust_outfiles' type='list' label='Adjust outfiles'>
1008 <data name='mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.mperm' label='${tool.name}: Association Max(T) permutation test'> 1036 <discover_datasets directory='adjust_out' pattern='__name_and_ext__'/>
1009 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and not functions['assoc']['fisher']</filter> 1037 <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes'</filter>
1010 </data> 1038 </collection>
1011 <data name='fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher' label='${tool.name}: Association Fisher'>
1012 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['fisher']</filter>
1013 </data>
1014 <data name='fisher_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.perm' label='${tool.name}: Association Fisher perm'>
1015 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and functions['assoc']['fisher']</filter>
1016 </data>
1017 <data name='fisher_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.mperm' label='${tool.name}: Association Fisher mperm'>
1018 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'mperm' and functions['assoc']['fisher']</filter>
1019 </data>
1020
1021 <!--adjust-->
1022 <data name='adjust' format='tabular' from_work_dir='plink_output/plink_output.assoc.adjusted' label='${tool.name}: Adjusted'>
1023 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and not functions['assoc']['fisher']</filter>
1024 </data>
1025 <data name='adjust_fisher' format='tabular' from_work_dir='plink_output/plink_output.assoc.fisher.adjusted' label='${tool.name}: Fisher Adjusted'>
1026 <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['adjust']['adjust'] == 'Yes' and functions['assoc']['fisher']</filter>
1027 </data>
1028 <data name='adjust_logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.adjusted' label='${tool.name}: Logistic Adjusted'>
1029 <filter>functions['func'] == 'association' and functions['adjust']['adjust'] == 'Yes' and functions['logistic']['logistic'] == 'Yes'</filter>
1030 </data>
1031
1032 <!-- <data name='linear' format='tabular' from_work_dir='plink_output/plink_output.assoc.linenar' label='${tool.name}: Linear Regression'>
1033 <filter>functions['func'] == 'association' and functions.func.association.linear['linear'] == 'Yes'</filter>
1034 </data> -->
1035
1036 <!--Logistic--> 1039 <!--Logistic-->
1037 <data name='logistic' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic' label='${tool.name}: Logistic Regression'> 1040 <collection name='log_outfiles' type='list' label='Logistic outfiles'>
1038 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter> 1041 <discover_datasets directory='logistic_out' pattern='__name_and_ext__'/>
1039 </data> 1042 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes'</filter>
1040 <data name='logistic_perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.perm' label='${tool.name}: Logistic Association Monte Carlo'> 1043 </collection>
1041 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'perm'</filter>
1042 </data>
1043 <data name='logistic_mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.logistic.mperm' label='${tool.name}: Logistic Association Max(T) permutation test'>
1044 <filter>functions['func'] == 'association' and functions['logistic']['logistic'] == 'Yes' and functions['logistic']['perm']['perm'] == 'mperm'</filter>
1045 </data>
1046
1047 <!--Link--> 1044 <!--Link-->
1048 <data name='prune_in' format='tabular' from_work_dir='plink_output/plink_output.prune.in' label='${tool.name}: Prune In'> 1045 <data name='prune_in' format='tabular' from_work_dir='plink_output/plink_output.prune.in' label='${tool.name}: Prune In'>
1049 <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter> 1046 <filter>functions['func'] == 'link' and functions['set_indep']['choice'] == 'Yes'</filter>
1050 </data> 1047 </data>
1051 <data name='prune_out' format='tabular' from_work_dir='plink_output/plink_output.prune.out' label='${tool.name}: Prune Out'> 1048 <data name='prune_out' format='tabular' from_work_dir='plink_output/plink_output.prune.out' label='${tool.name}: Prune Out'>
1289 <output name='cluster2' value='plink.cluster2' compare='sim_size'/> 1286 <output name='cluster2' value='plink.cluster2' compare='sim_size'/>
1290 <output name='cluster3' value='plink.cluster3' compare='sim_size'/> 1287 <output name='cluster3' value='plink.cluster3' compare='sim_size'/>
1291 <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/> 1288 <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/>
1292 </test> 1289 </test>
1293 1290
1294 <test expect_num_outputs='11'> 1291 <test expect_num_outputs='8'>
1295 <section name='inputs'> 1292 <section name='inputs'>
1296 <conditional name='inputs'> 1293 <conditional name='inputs'>
1297 <param name='filetype' value='bfile'/> 1294 <param name='filetype' value='bfile'/>
1298 <param name='bed' value='plink.bed'/> 1295 <param name='bed' value='plink.bed'/>
1299 <param name='bim' value='plink.bim'/> 1296 <param name='bim' value='plink.bim'/>
1331 <output_collection name='plink_out' type='list'> 1328 <output_collection name='plink_out' type='list'>
1332 <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/> 1329 <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/>
1333 <element name='plink_bim' file='out.assoc.bim'/> 1330 <element name='plink_bim' file='out.assoc.bim'/>
1334 <element name='plink_fam' file='out.assoc.fam'/> 1331 <element name='plink_fam' file='out.assoc.fam'/>
1335 </output_collection> 1332 </output_collection>
1336 <output name='fisher' value="out.assoc.fisher"/> 1333 <output_collection name='assoc_outfiles' type='list' count='2'>
1337 <output name='adjust_fisher' value="out.assoc.fisher.adjusted" sort="True" /> 1334 <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/>
1338 <output name='fisher_mperm' value="out.assoc.fisher.mperm" compare='sim_size'/> 1335 <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/>
1339 <output name='logistic' value="out.assoc.logistic"/> 1336 </output_collection>
1340 <output name='adjust_logistic' value="out.assoc.logistic.adjusted"/> 1337 <output_collection name='adjust_outfiles' type='list' count='1'>
1341 <output name='logistic_perm' value="out.assoc.logistic.perm" compare='sim_size'/> 1338 <element name='plink_output.assoc.fisher.adjusted' value='out.assoc.fisher.adjusted' compare='sim_size' />
1339 </output_collection>
1340 <output_collection name='log_outfiles' type='list' count='3'>
1341 <element name='plink_output.assoc.logistic' value='out.assoc.logistic'/>
1342 <element name='plink_output.assoc.logistic.adjusted' value='out.assoc.logistic.adjusted'/>
1343 <element name='plink_output.assoc.logistic.perm' value='out.assoc.logistic.perm' compare='sim_size'/>
1344 </output_collection>
1342 </test> 1345 </test>
1343 1346
1344 <test expect_num_outputs='6'> 1347 <test expect_num_outputs='6'>
1345 <section name='inputs'> 1348 <section name='inputs'>
1346 <conditional name='inputs'> 1349 <conditional name='inputs'>