diff plink.xml @ 8:16d22eee0fe3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"

--- 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>