Mercurial > repos > iuc > plink
diff plink.xml @ 8:16d22eee0fe3 draft
"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 |
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--- a/plink.xml Mon Oct 05 16:08:24 2020 +0000 +++ b/plink.xml Thu Dec 02 16:20:30 2021 +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@'>2</token> + <token name='@VERSION_SUFFIX@'>3</token> <xml name='template_sanitizer'> <sanitizer> <valid initial='default'> @@ -38,6 +38,9 @@ </sanitizer> </xml> </macros> + <xrefs> + <xref type="bio.tools">plink</xref> + </xrefs> <requirements> <requirement type='package' version='1.90b6.18'>plink</requirement> </requirements> @@ -354,7 +357,7 @@ $functions.logistic.beta $functions.logistic.intercept #end if - + --lambda $functions.lambda #elif $functions.func == 'ibd': #if $functions.genome.output_genome: --genome @@ -443,11 +446,11 @@ <when value='filtering'> <conditional name='id_list'> <param name='func' type='select' label='ID list functions'> - <option value='none'/> - <option value='keep'/> - <option value='keep-fam'/> - <option value='remove'/> - <option value='remove-fam'/> + <option value='none'>None</option> + <option value='keep'>Keep by sample IDs</option> + <option value='keep-fam'>Keep by family IDs</option> + <option value='remove'>Remove by sample IDs</option> + <option value='remove-fam'>Remove by family IDs</option> </param> <when value='none'/> <when value='keep'> @@ -465,9 +468,9 @@ </conditional> <conditional name='extraction'> <param name='ex_func' type='select' label='ID extraction functions'> - <option value='none'/> - <option value='extract'/> - <option value='exclude'/> + <option value='none'>None</option> + <option value='extract'>Keep by variant IDs</option> + <option value='exclude'>Remove by variant IDs </option> </param> <when value='none'/> <when value='extract'> @@ -568,8 +571,8 @@ </conditional> <conditional name='thinning'> <param name='thinning' type='select' label='Arbitrary thinning'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -620,8 +623,8 @@ </section> <conditional name='hwe'> <param name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -637,8 +640,8 @@ </conditional> <conditional name='sex_founder_filter'> <param name='filter' type='select' label='Filter on sex and/or founders'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -663,8 +666,8 @@ <when value='data_manage'> <conditional name='bmerge'> <param name='set' type='select' label='Merge plink tilesets'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -805,8 +808,8 @@ <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/> <conditional name='cluster'> <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -817,8 +820,8 @@ </param> <conditional name='mds'> <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -837,7 +840,7 @@ <conditional name='assoc'> <param name='assoc' label='Perform 1df chi-square allelic test' type='select'> <option value=''>No</option> - <option value='Yes'/> + <option value='Yes'>Yes</option> </param> <when value=''/> <when value='Yes'> @@ -865,8 +868,8 @@ </conditional> <conditional name='adjust'> <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -921,8 +924,8 @@ </conditional> --> <conditional name='logistic'> <param name='logistic' type='select' label='Perform logistic regression and return report'> - <option value='No'/> - <option value='Yes'/> + <option value='No'>No</option> + <option value='Yes'>Yes</option> </param> <when value='No'/> <when value='Yes'> @@ -967,7 +970,7 @@ <conditional name='genome'> <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'> <option value=''>No</option> - <option value='Yes'/> + <option value='Yes'>Yes</option> </param> <when value=''/> <when value='Yes'> @@ -1373,4 +1376,4 @@ <citations> <citation type='doi'>10.1186/s13742-015-0047-8</citation> </citations> -</tool> \ No newline at end of file +</tool>