--- a/mageck_test.xml	Sat Jan 05 05:47:18 2019 -0500
+++ b/mageck_test.xml	Wed Apr 01 10:10:28 2020 +0000
@@ -112,7 +112,7 @@
             <option value="holm">Holm</option>
             <option value="pounds">Pounds</option>
         </param>
-        <param name="var_samples" argument="--variance-from-all-samples" type="boolean" truevalue="--variance-from-all-samples" falsevalue="" checked="false" optional="true" label="Estimate the variance from all samples, instead of from only control samples" help="Use this option only if you believe there are relatively few essential sgRNAs or genes between control and treatment samples" />
+        <param name="var_samples" argument="--variance-estimation-samples" type="boolean" truevalue="--variance-estimation-samples" falsevalue="" checked="false" optional="true" label="Estimate variances from designated samples" help="To use, specify sample label or sample index for estimating variances, separated by comma (,). See -t/--treatment-id option for specifying samples." />
         <expand macro="sort_criteria" />
         <param name="remove_zero" argument="--remove-zero" type="select" optional="true" label="Remove zero" help="Remove sgRNAs whose mean value is zero in Control, Treatment, Both control/treatment, or Any control/treatment sample. Default: Both (remove those sgRNAs that are zero in both control and treatment samples)" >
             <option value="none" >None</option>