# HG changeset patch
# User iuc
# Date 1585736124 14400
# Node ID 9b4f4533c9ee606edea015a91c7422b09920c15b
# Parent  688a8eccea71cb52df234183c00a28e8b45bb86b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit e9c464070ad7c01b830345a550477e8dfdcac5ae"

diff -r 688a8eccea71 -r 9b4f4533c9ee mageck_macros.xml
--- a/mageck_macros.xml	Sat Jan 05 05:49:38 2019 -0500
+++ b/mageck_macros.xml	Wed Apr 01 06:15:24 2020 -0400
@@ -1,13 +1,14 @@
 <?xml version="1.0"?>
 <macros>
 
-    <token name="@VERSION@">0.5.8</token>
+    <token name="@VERSION@">0.5.9.2</token>
 
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">mageck</requirement>
-            <requirement type="package" version="3.0.1">r-gplots</requirement>
-            <requirement type="package" version="1.8_3">r-xtable</requirement>
+            <requirement type="package" version="3.0.3">r-gplots</requirement>
+            <requirement type="package" version="1.8_4">r-xtable</requirement>
+            <requirement type="package" version="3.3.0">r-ggplot2</requirement>
             <yield/>
         </requirements>
     </xml>
diff -r 688a8eccea71 -r 9b4f4533c9ee mageck_test.xml
--- a/mageck_test.xml	Sat Jan 05 05:49:38 2019 -0500
+++ b/mageck_test.xml	Wed Apr 01 06:15:24 2020 -0400
@@ -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>