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plink: add lambda to commandline #4244

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Dec 2, 2021
Merged

plink: add lambda to commandline #4244

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fd7b5c4
plink: add lambda to commandline
bernt-matthias Nov 26, 2021
ef763ae
bump
bgruening Nov 27, 2021
5de0779
fix xref lint error
bgruening Nov 27, 2021
69dfa5b
add option text for all options
bernt-matthias Dec 2, 2021
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64 changes: 32 additions & 32 deletions tools/plink/plink.xml
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Original file line number Diff line number Diff line change
@@ -1,10 +1,7 @@
<tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
<xrefs>
<xref type="bio.tools">plink</xref>
</xrefs>
<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'>
Expand Down Expand Up @@ -41,6 +38,9 @@
</sanitizer>
</xml>
</macros>
<xrefs>
<xref type="bio.tools">plink</xref>
</xrefs>
<requirements>
<requirement type='package' version='1.90b6.18'>plink</requirement>
</requirements>
Expand Down Expand Up @@ -357,7 +357,7 @@
$functions.logistic.beta
$functions.logistic.intercept
#end if

--lambda $functions.lambda
#elif $functions.func == 'ibd':
#if $functions.genome.output_genome:
--genome
Expand Down Expand Up @@ -446,11 +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'>
Expand All @@ -468,9 +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'>
Expand Down Expand Up @@ -571,8 +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'>
Expand Down Expand Up @@ -623,8 +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'>
Expand All @@ -640,8 +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'>
Expand All @@ -666,8 +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'>
Expand Down Expand Up @@ -808,8 +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'>
Expand All @@ -820,8 +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'>
Expand All @@ -840,7 +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'>
Expand Down Expand Up @@ -868,8 +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'>
Expand Down Expand Up @@ -924,8 +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'>
Expand Down Expand Up @@ -970,7 +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'>
Expand Down Expand Up @@ -1376,4 +1376,4 @@
<citations>
<citation type='doi'>10.1186/s13742-015-0047-8</citation>
</citations>
</tool>
</tool>
100 changes: 50 additions & 50 deletions tools/plink/test-data/out.assoc.fisher.adjusted
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,51 +1,51 @@
CHR SNP UNADJ GC QQ BONF HOLM SIDAK_SS SIDAK_SD FDR_BH FDR_BY
1 snp13 1.369 1.369 2 0 0 0.05171 0.05171 0.05883 0
1 snp45 1.276 1.276 1.523 0 0 0.02964 0.03136 0.05883 0
1 snp22 1.188 1.188 1.301 0 0 0.01545 0.01771 0.05883 0
1 snp1 1.019 1.019 1.155 0 0 0.002837 0.003842 0.05883 0
1 snp5 0.8623 0.8623 1.046 0 0 0.0002697 0.000487 0.05883 0
1 snp15 0.7893 0.7893 0.9586 0 0 6.152e-05 0.0001493 0.05883 0
1 snp33 0.7185 0.7185 0.8861 0 0 1.07e-05 3.822e-05 0.05883 0
1 snp36 0.717 0.717 0.8239 0 0 1.028e-05 3.822e-05 0.05883 0
1 snp21 0.6489 0.6489 0.7696 0 0 1.314e-06 1.004e-05 0.05883 0
1 snp18 0.6487 0.6487 0.7212 0 0 1.303e-06 1.004e-05 0.05883 0
1 snp23 0.5838 0.5838 0.6778 0 0 1.195e-07 2.452e-06 0.05883 0
1 snp12 0.5228 0.5228 0.6383 0 0 7.772e-09 3.935e-07 0.05883 0
1 snp41 0.5219 0.5219 0.6021 0 0 7.455e-09 3.935e-07 0.05883 0
1 snp17 0.4642 0.4642 0.5686 0 0 3.191e-10 7.563e-08 0.05883 0
1 snp2 0.4625 0.4625 0.5376 0 0 2.869e-10 7.563e-08 0.05883 0
1 snp35 0.4622 0.4622 0.5086 0 0 2.825e-10 7.563e-08 0.05883 0
1 snp28 0.4103 0.4103 0.4815 0 0 8.864e-12 2.336e-08 0.05883 0
1 snp38 0.4069 0.4069 0.4559 0 0 6.895e-12 2.336e-08 0.05883 0
1 snp43 0.4064 0.4064 0.4318 0 0 6.662e-12 2.336e-08 0.05883 0
1 snp8 0.4062 0.4062 0.4089 0 0 6.539e-12 2.336e-08 0.05883 0
1 snp9 0.3537 0.3537 0.3872 0 0 8.607e-14 1.038e-08 0.05883 0
1 snp19 0.3524 0.3524 0.3665 0 0 7.618e-14 1.038e-08 0.05883 0
1 snp44 0.3523 0.3523 0.3468 0 0 7.575e-14 1.038e-08 0.05883 0
1 snp31 0.352 0.352 0.3279 0 0 7.348e-14 1.038e-08 0.05883 0
1 snp29 0.3018 0.3018 0.3098 0 0 4.339e-16 6.787e-09 0.05883 0
1 snp30 0.3011 0.3011 0.2924 0 0 3.857e-16 6.787e-09 0.05883 0
1 snp42 0.3011 0.3011 0.2757 0 0 3.857e-16 6.787e-09 0.05883 0
1 snp49 0.3011 0.3011 0.2596 0 0 3.857e-16 6.787e-09 0.05883 0
1 snp34 0.253 0.253 0.2441 0 0 0 6.732e-09 0.05883 0
1 snp37 0.2529 0.2529 0.2291 0 0 0 6.732e-09 0.05883 0
1 snp40 0.2528 0.2528 0.2147 0 0 0 6.732e-09 0.05883 0
1 snp20 0.2526 0.2526 0.2007 0 0 0 6.732e-09 0.05883 0
1 snp48 0.2072 0.2072 0.1871 0 0 0 6.732e-09 0.05814 0
1 snp14 0.207 0.207 0.1739 0 0 0 6.732e-09 0.05814 0
1 snp0 0.1643 0.1643 0.1612 0 0 0 4.076e-09 0.05814 0
1 snp11 0.1642 0.1642 0.1487 0 0 0 4.076e-09 0.05814 0
1 snp7 0.1639 0.1639 0.1367 0 0 0 4.076e-09 0.05814 0
1 snp26 0.1638 0.1638 0.1249 0 0 0 4.076e-09 0.05814 0
1 snp32 0.1235 0.1235 0.1135 0 0 0 4.076e-09 0.05814 0
1 snp16 0.1235 0.1235 0.1024 0 0 0 4.076e-09 0.05814 0
1 snp25 0.1234 0.1234 0.09151 0 0 0 4.076e-09 0.05814 0
1 snp39 0.1233 0.1233 0.08092 0 0 0 4.076e-09 0.05814 0
1 snp46 0.1233 0.1233 0.07058 0 0 0 4.076e-09 0.05814 0
1 snp47 0.08552 0.08552 0.06048 0 0 0 4.076e-09 0.05814 0
1 snp3 0.08512 0.08512 0.05061 0 0 0 4.076e-09 0.05814 0
1 snp27 0.08512 0.08512 0.04096 0 0 0 4.076e-09 0.05814 0
1 snp4 0.08501 0.08501 0.03152 0 0 0 4.076e-09 0.05814 0
1 snp24 0.04939 0.04939 0.02228 0 0 0 4.076e-09 0.03167 0
1 snp6 0.0159 0.0159 0.01323 0 0 0 4.076e-09 0.01585 0
1 snp10 0.01585 0.01585 0.004365 0 0 0 4.076e-09 0.01585 0
1 snp13 1.605 1.605 2 0 0 0.1455 0.1455 0.1672 0
1 snp45 1.495 1.495 1.523 0 0 0.09512 0.09865 0.1672 0
1 snp22 1.389 1.389 1.301 0 0 0.0577 0.06309 0.1672 0
1 snp1 1.187 1.187 1.155 0 0 0.01536 0.01887 0.09243 0
1 snp5 1.001 1.001 1.046 0 0 0.00228 0.003475 0.09243 0
1 snp15 0.9147 0.9147 0.9586 0 0 0.0006612 0.001266 0.09243 0
1 snp33 0.8308 0.8308 0.8861 0 0 0.0001477 0.0003853 0.09243 0
1 snp36 0.8291 0.8291 0.8239 0 0 0.0001428 0.0003853 0.09243 0
1 snp21 0.7487 0.7487 0.7696 0 0 2.357e-05 0.0001135 0.09243 0
1 snp18 0.7485 0.7485 0.7212 0 0 2.34e-05 0.0001135 0.09243 0
1 snp23 0.6721 0.6721 0.6778 0 0 2.771e-06 3.032e-05 0.09243 0
1 snp12 0.6004 0.6004 0.6383 0 0 2.311e-07 5.548e-06 0.09243 0
1 snp41 0.5995 0.5995 0.6021 0 0 2.225e-07 5.548e-06 0.09243 0
1 snp17 0.5319 0.5319 0.5686 0 0 1.212e-08 1.116e-06 0.09243 0
1 snp2 0.5299 0.5299 0.5376 0 0 1.098e-08 1.116e-06 0.09243 0
1 snp35 0.5296 0.5296 0.5086 0 0 1.082e-08 1.116e-06 0.09243 0
1 snp28 0.4689 0.4689 0.4815 0 0 4.225e-10 3.233e-07 0.09243 0
1 snp38 0.465 0.465 0.4559 0 0 3.334e-10 3.233e-07 0.09243 0
1 snp43 0.4644 0.4644 0.4318 0 0 3.228e-10 3.233e-07 0.09243 0
1 snp8 0.4641 0.4641 0.4089 0 0 3.171e-10 3.233e-07 0.09243 0
1 snp9 0.4031 0.4031 0.3872 0 0 5.202e-12 1.216e-07 0.09243 0
1 snp19 0.4016 0.4016 0.3665 0 0 4.628e-12 1.216e-07 0.09243 0
1 snp44 0.4015 0.4015 0.3468 0 0 4.604e-12 1.216e-07 0.09243 0
1 snp31 0.4011 0.4011 0.3279 0 0 4.473e-12 1.216e-07 0.09243 0
1 snp29 0.343 0.343 0.3098 0 0 3.158e-14 6.397e-08 0.09243 0
1 snp30 0.3422 0.3422 0.2924 0 0 2.917e-14 6.397e-08 0.09243 0
1 snp42 0.3422 0.3422 0.2757 0 0 2.917e-14 6.397e-08 0.09243 0
1 snp49 0.3422 0.3422 0.2596 0 0 2.917e-14 6.397e-08 0.09243 0
1 snp34 0.2867 0.2867 0.2441 0 0 4.822e-17 4.889e-08 0.09243 0
1 snp37 0.2866 0.2866 0.2291 0 0 4.822e-17 4.889e-08 0.09243 0
1 snp40 0.2864 0.2864 0.2147 0 0 4.822e-17 4.889e-08 0.09243 0
1 snp20 0.2862 0.2862 0.2007 0 0 4.822e-17 4.889e-08 0.09243 0
1 snp48 0.234 0.234 0.1871 0 0 0 4.889e-08 0.07281 0
1 snp14 0.2338 0.2338 0.1739 0 0 0 4.889e-08 0.07281 0
1 snp0 0.185 0.185 0.1612 0 0 0 1.905e-08 0.07281 0
1 snp11 0.1848 0.1848 0.1487 0 0 0 1.905e-08 0.07281 0
1 snp7 0.1845 0.1845 0.1367 0 0 0 1.905e-08 0.07281 0
1 snp26 0.1845 0.1845 0.1249 0 0 0 1.905e-08 0.07281 0
1 snp32 0.1386 0.1386 0.1135 0 0 0 1.905e-08 0.07281 0
1 snp16 0.1386 0.1386 0.1024 0 0 0 1.905e-08 0.07281 0
1 snp25 0.1384 0.1384 0.09151 0 0 0 1.905e-08 0.07281 0
1 snp39 0.1384 0.1384 0.08092 0 0 0 1.905e-08 0.07281 0
1 snp46 0.1383 0.1383 0.07058 0 0 0 1.905e-08 0.07281 0
1 snp47 0.09563 0.09563 0.06048 0 0 0 1.905e-08 0.06819 0
1 snp3 0.09519 0.09519 0.05061 0 0 0 1.905e-08 0.06819 0
1 snp27 0.09519 0.09519 0.04096 0 0 0 1.905e-08 0.06819 0
1 snp4 0.09506 0.09506 0.03152 0 0 0 1.905e-08 0.06819 0
1 snp24 0.05503 0.05503 0.02228 0 0 0 1.905e-08 0.03731 0
1 snp6 0.01765 0.01765 0.01323 0 0 0 1.905e-08 0.01759 0
1 snp10 0.01759 0.01759 0.004365 0 0 0 1.905e-08 0.01759 0
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