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comparison plink.xml @ 8:16d22eee0fe3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
author iuc
date Thu, 02 Dec 2021 16:20:30 +0000
parents 66b35562554d
children 272aca44b3dd
comparison
equal deleted inserted replaced
7:66b35562554d 8:16d22eee0fe3
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@'>2</token> 4 <token name='@VERSION_SUFFIX@'>3</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='@' />
36 <add value=' '/> 36 <add value=' '/>
37 </valid> 37 </valid>
38 </sanitizer> 38 </sanitizer>
39 </xml> 39 </xml>
40 </macros> 40 </macros>
41 <xrefs>
42 <xref type="bio.tools">plink</xref>
43 </xrefs>
41 <requirements> 44 <requirements>
42 <requirement type='package' version='1.90b6.18'>plink</requirement> 45 <requirement type='package' version='1.90b6.18'>plink</requirement>
43 </requirements> 46 </requirements>
44 <command detect_errors='exit_code'><![CDATA[ 47 <command detect_errors='exit_code'><![CDATA[
45 48
352 $functions.logistic.sex_covar 355 $functions.logistic.sex_covar
353 $functions.logistic.interaction 356 $functions.logistic.interaction
354 $functions.logistic.beta 357 $functions.logistic.beta
355 $functions.logistic.intercept 358 $functions.logistic.intercept
356 #end if 359 #end if
357 360 --lambda $functions.lambda
358 #elif $functions.func == 'ibd': 361 #elif $functions.func == 'ibd':
359 #if $functions.genome.output_genome: 362 #if $functions.genome.output_genome:
360 --genome 363 --genome
361 #for $type in $functions.genome.modifiers 364 #for $type in $functions.genome.modifiers
362 $type 365 $type
441 <!-- <option value='rerun'>Rerun</option> --> 444 <!-- <option value='rerun'>Rerun</option> -->
442 </param> 445 </param>
443 <when value='filtering'> 446 <when value='filtering'>
444 <conditional name='id_list'> 447 <conditional name='id_list'>
445 <param name='func' type='select' label='ID list functions'> 448 <param name='func' type='select' label='ID list functions'>
446 <option value='none'/> 449 <option value='none'>None</option>
447 <option value='keep'/> 450 <option value='keep'>Keep by sample IDs</option>
448 <option value='keep-fam'/> 451 <option value='keep-fam'>Keep by family IDs</option>
449 <option value='remove'/> 452 <option value='remove'>Remove by sample IDs</option>
450 <option value='remove-fam'/> 453 <option value='remove-fam'>Remove by family IDs</option>
451 </param> 454 </param>
452 <when value='none'/> 455 <when value='none'/>
453 <when value='keep'> 456 <when value='keep'>
454 <param format='tabular,tsv' name='file' type='data' label='Keep file.' help='Accepts one or more space/tab-delimited text files with sample IDs, and removes all unlisted samples from the current analysis;'/> 457 <param format='tabular,tsv' name='file' type='data' label='Keep file.' help='Accepts one or more space/tab-delimited text files with sample IDs, and removes all unlisted samples from the current analysis;'/>
455 </when> 458 </when>
463 <param format='tabular,tsv' name='file' type='data' label='Remove-fam file' help='Acceptz text files with family IDs in the first column, and removes entire families.'/> 466 <param format='tabular,tsv' name='file' type='data' label='Remove-fam file' help='Acceptz text files with family IDs in the first column, and removes entire families.'/>
464 </when> 467 </when>
465 </conditional> 468 </conditional>
466 <conditional name='extraction'> 469 <conditional name='extraction'>
467 <param name='ex_func' type='select' label='ID extraction functions'> 470 <param name='ex_func' type='select' label='ID extraction functions'>
468 <option value='none'/> 471 <option value='none'>None</option>
469 <option value='extract'/> 472 <option value='extract'>Keep by variant IDs</option>
470 <option value='exclude'/> 473 <option value='exclude'>Remove by variant IDs </option>
471 </param> 474 </param>
472 <when value='none'/> 475 <when value='none'/>
473 <when value='extract'> 476 <when value='extract'>
474 <param format='txt' name='file' type='data' label='Extract' help='Accepts one or more text file(s) with variant IDs , and removes all unlisted variants from the current analysis'/> 477 <param format='txt' name='file' type='data' label='Extract' help='Accepts one or more text file(s) with variant IDs , and removes all unlisted variants from the current analysis'/>
475 <param type='boolean' name='range' truevalue='range' falsevalue='' help='Input file is input in set range format.'/> 478 <param type='boolean' name='range' truevalue='range' falsevalue='' help='Input file is input in set range format.'/>
566 </param> 569 </param>
567 </when> 570 </when>
568 </conditional> 571 </conditional>
569 <conditional name='thinning'> 572 <conditional name='thinning'>
570 <param name='thinning' type='select' label='Arbitrary thinning'> 573 <param name='thinning' type='select' label='Arbitrary thinning'>
571 <option value='No'/> 574 <option value='No'>No</option>
572 <option value='Yes'/> 575 <option value='Yes'>Yes</option>
573 </param> 576 </param>
574 <when value='No'/> 577 <when value='No'/>
575 <when value='Yes'> 578 <when value='Yes'>
576 <param name='thin' type='float' label='Thin' min='0' max='1.0' help='Removes variants at random by retaining each variant with probability p' optional='true'/> 579 <param name='thin' type='float' label='Thin' min='0' max='1.0' help='Removes variants at random by retaining each variant with probability p' optional='true'/>
577 <param name='thin_count' type='integer' label='Thin Count' help='Removes variants at random until only n remain' min='1' optional='true'/> 580 <param name='thin_count' type='integer' label='Thin Count' help='Removes variants at random until only n remain' min='1' optional='true'/>
618 <param name='mac' type='integer' label='Minimum allele count' min='1' help='Filters out all variants with allele counts below the provided threshold' optional='true'/> 621 <param name='mac' type='integer' label='Minimum allele count' min='1' help='Filters out all variants with allele counts below the provided threshold' optional='true'/>
619 <param name='max_mac' type='integer' label='Maximum allele count' min='0' help='filters out all variants with allele counts above the provided threshold' optional='true'/> 622 <param name='max_mac' type='integer' label='Maximum allele count' min='0' help='filters out all variants with allele counts above the provided threshold' optional='true'/>
620 </section> 623 </section>
621 <conditional name='hwe'> 624 <conditional name='hwe'>
622 <param name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'> 625 <param name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'>
623 <option value='No'/> 626 <option value='No'>No</option>
624 <option value='Yes'/> 627 <option value='Yes'>Yes</option>
625 </param> 628 </param>
626 <when value='No'/> 629 <when value='No'/>
627 <when value='Yes'> 630 <when value='Yes'>
628 <param name='hwe_val' type='float' label='Hardy-Weinberg Equilibrium' help='Filters out all variants which have Hardy-Weinberg equilibrium exact test 631 <param name='hwe_val' type='float' label='Hardy-Weinberg Equilibrium' help='Filters out all variants which have Hardy-Weinberg equilibrium exact test
629 p-value below the provided threshold. It is recommended setting a low threshold—serious genotyping errors often yield extreme p-values like 1e-501 which 632 p-value below the provided threshold. It is recommended setting a low threshold—serious genotyping errors often yield extreme p-values like 1e-501 which
635 </param> 638 </param>
636 </when> 639 </when>
637 </conditional> 640 </conditional>
638 <conditional name='sex_founder_filter'> 641 <conditional name='sex_founder_filter'>
639 <param name='filter' type='select' label='Filter on sex and/or founders'> 642 <param name='filter' type='select' label='Filter on sex and/or founders'>
640 <option value='No'/> 643 <option value='No'>No</option>
641 <option value='Yes'/> 644 <option value='Yes'>Yes</option>
642 </param> 645 </param>
643 <when value='No'/> 646 <when value='No'/>
644 <when value='Yes'> 647 <when value='Yes'>
645 <param name='sex_select' type='select' label='Sex select' help='Filter by phenotypes, experiment, and founder state.'> 648 <param name='sex_select' type='select' label='Sex select' help='Filter by phenotypes, experiment, and founder state.'>
646 <option value=''>Do not specifically filter out based on sex or founders</option> 649 <option value=''>Do not specifically filter out based on sex or founders</option>
661 </conditional> 664 </conditional>
662 </when> 665 </when>
663 <when value='data_manage'> 666 <when value='data_manage'>
664 <conditional name='bmerge'> 667 <conditional name='bmerge'>
665 <param name='set' type='select' label='Merge plink tilesets'> 668 <param name='set' type='select' label='Merge plink tilesets'>
666 <option value='No'/> 669 <option value='No'>No</option>
667 <option value='Yes'/> 670 <option value='Yes'>Yes</option>
668 </param> 671 </param>
669 <when value='No'/> 672 <when value='No'/>
670 <when value='Yes'> 673 <when value='Yes'>
671 <param format='binary' name='bed' type='data' label='plink bed file'/> 674 <param format='binary' name='bed' type='data' label='plink bed file'/>
672 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> 675 <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/>
803 </when> 806 </when>
804 <when value='stratification'> 807 <when value='stratification'>
805 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/> 808 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/>
806 <conditional name='cluster'> 809 <conditional name='cluster'>
807 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'> 810 <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'>
808 <option value='No'/> 811 <option value='No'>No</option>
809 <option value='Yes'/> 812 <option value='Yes'>Yes</option>
810 </param> 813 </param>
811 <when value='No'/> 814 <when value='No'/>
812 <when value='Yes'> 815 <when value='Yes'>
813 <param name='modifiers' type='select' label='Cluster flag modifiers' multiple='true' display='checkboxes' optional='true'> 816 <param name='modifiers' type='select' label='Cluster flag modifiers' multiple='true' display='checkboxes' optional='true'>
814 <option value='cc'>Prevent two all-case or two all-control clusters from being merged.</option> 817 <option value='cc'>Prevent two all-case or two all-control clusters from being merged.</option>
815 <option value='group-avg'>By default, the distance between two clusters is defined as the maximum pairwise distance between a member of the first cluster and a member of the second cluster. Cause average pairwise distance to be used instead.</option> 818 <option value='group-avg'>By default, the distance between two clusters is defined as the maximum pairwise distance between a member of the first cluster and a member of the second cluster. Cause average pairwise distance to be used instead.</option>
816 <option value='missing'>Cause clustering to be based on identity-by-missingness</option> 819 <option value='missing'>Cause clustering to be based on identity-by-missingness</option>
817 </param> 820 </param>
818 <conditional name='mds'> 821 <conditional name='mds'>
819 <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'> 822 <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'>
820 <option value='No'/> 823 <option value='No'>No</option>
821 <option value='Yes'/> 824 <option value='Yes'>Yes</option>
822 </param> 825 </param>
823 <when value='No'/> 826 <when value='No'/>
824 <when value='Yes'> 827 <when value='Yes'>
825 <param name='dimensions' type='integer' label='Dimension count' value='10'/> 828 <param name='dimensions' type='integer' label='Dimension count' value='10'/>
826 <param name='modifiers' type='select' label='mds-plot flag modifiers' multiple='true' display='checkboxes' optional='true'> 829 <param name='modifiers' type='select' label='mds-plot flag modifiers' multiple='true' display='checkboxes' optional='true'>
835 </when> 838 </when>
836 <when value='association'> 839 <when value='association'>
837 <conditional name='assoc'> 840 <conditional name='assoc'>
838 <param name='assoc' label='Perform 1df chi-square allelic test' type='select'> 841 <param name='assoc' label='Perform 1df chi-square allelic test' type='select'>
839 <option value=''>No</option> 842 <option value=''>No</option>
840 <option value='Yes'/> 843 <option value='Yes'>Yes</option>
841 </param> 844 </param>
842 <when value=''/> 845 <when value=''/>
843 <when value='Yes'> 846 <when value='Yes'>
844 <conditional name='perm'> 847 <conditional name='perm'>
845 <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'> 848 <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>
863 <param name='count' label='Counts' type='boolean' truevalue='counts' falsevalue='' checked='false' help='Report allele counts instead of frequencies'/> 866 <param name='count' label='Counts' type='boolean' truevalue='counts' falsevalue='' checked='false' help='Report allele counts instead of frequencies'/>
864 </when> 867 </when>
865 </conditional> 868 </conditional>
866 <conditional name='adjust'> 869 <conditional name='adjust'>
867 <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'> 870 <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'>
868 <option value='No'/> 871 <option value='No'>No</option>
869 <option value='Yes'/> 872 <option value='Yes'>Yes</option>
870 </param> 873 </param>
871 <when value='No'/> 874 <when value='No'/>
872 <when value='Yes'> 875 <when value='Yes'>
873 <param name='tests' label='Testing modifiers' type='select' multiple='true' display='checkboxes' optional='true'> 876 <param name='tests' label='Testing modifiers' type='select' multiple='true' display='checkboxes' optional='true'>
874 <option value='gc'>Use genomic-controlled p-values in the formulas</option> 877 <option value='gc'>Use genomic-controlled p-values in the formulas</option>
919 <param name='intercept' label='intercept' type='boolean' truevalue='intercept' falsevalue='' checked='false' help=''/> 922 <param name='intercept' label='intercept' type='boolean' truevalue='intercept' falsevalue='' checked='false' help=''/>
920 </when> 923 </when>
921 </conditional> --> 924 </conditional> -->
922 <conditional name='logistic'> 925 <conditional name='logistic'>
923 <param name='logistic' type='select' label='Perform logistic regression and return report'> 926 <param name='logistic' type='select' label='Perform logistic regression and return report'>
924 <option value='No'/> 927 <option value='No'>No</option>
925 <option value='Yes'/> 928 <option value='Yes'>Yes</option>
926 </param> 929 </param>
927 <when value='No'/> 930 <when value='No'/>
928 <when value='Yes'> 931 <when value='Yes'>
929 <conditional name='perm'> 932 <conditional name='perm'>
930 <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'> 933 <param name='perm' type='select' help='Request an adaptive or max(T) permutation test on the additive effect.'>
965 </when> --> 968 </when> -->
966 <when value='ibd'> 969 <when value='ibd'>
967 <conditional name='genome'> 970 <conditional name='genome'>
968 <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'> 971 <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'>
969 <option value=''>No</option> 972 <option value=''>No</option>
970 <option value='Yes'/> 973 <option value='Yes'>Yes</option>
971 </param> 974 </param>
972 <when value=''/> 975 <when value=''/>
973 <when value='Yes'> 976 <when value='Yes'>
974 <param name='min' type='float' label='min' min='0' max='1.0' help='Minimum PI_HAT value' optional='true'/> 977 <param name='min' type='float' label='min' min='0' max='1.0' help='Minimum PI_HAT value' optional='true'/>
975 <param name='max' type='float' label='max' min='0' max='1.0' help='Maximum PI_HAT value' optional='true'/> 978 <param name='max' type='float' label='max' min='0' max='1.0' help='Maximum PI_HAT value' optional='true'/>