Merge pull request #3210 from astrovsky01/plink1.9_minor

Plink default blank flags
galaxyproject · Sep 25, 2020 · fa78db0 · fa78db0
2 parents 07c2255 + 5133a24
commit fa78db0
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/tools/plink/plink.xml b/tools/plink/plink.xml
@@ -614,6 +614,7 @@
                     <when value='No'/>
                     <when value='Yes'>
                         <param name='sex_select' type='select' label='Sex select' help='Filter by phenotypes, experiment, and founder state.'>
+                            <option value=''>Do not specifically filter out based on sex or founders</option>
                             <option value='--filter-cases'>Only include cases</option>
                             <option value='--filter-controls'>Only include controls</option>
                             <option value='--filter-males'>Only include males</option>
@@ -622,6 +623,7 @@
                             <option value='--filter-nonfounders'>Only include samples with at least one known parental ID</option>
                         </param>
                         <param name='no_sex_select' type='select' label='No sex settings' optional='true' help='How to deal with ambiguous sex phenotypes'>
+                            <option value=''>Change nothing with regards to ambiguous sex samples</option>
                             <option value='--allow-no-sex'>Prevent samples with ambiguous sex frim having their phenotypes set to missing when analysis commands are run</option>
                             <option value='--must-have-sex'>Force phenotypes of ambiguous-sex samples to missing in output</option>
                         </param>