# HG changeset patch
# User iuc
# Date 1518882101 18000
# Node ID 93f268840b0c067b2e8f3a5525ee410d4634d90b
# Parent  eab37e8fea75c05a1aa5383cd2ea59acf6e1f769
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7

diff -r eab37e8fea75 -r 93f268840b0c mageck_mle.xml
--- a/mageck_mle.xml	Wed Feb 14 06:42:36 2018 -0500
+++ b/mageck_mle.xml	Sat Feb 17 10:41:41 2018 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="mageck_mle" name="MAGeCK mle" version="@VERSION@" >
+<tool id="mageck_mle" name="MAGeCK mle" version="@VERSION@.1" >
     <description>- perform maximum-likelihood estimation of gene essentiality scores</description>
     <macros>
         <import>mageck_macros.xml</import>
@@ -74,7 +74,7 @@
                 <option value="control">Control</option>
             </param>
             <param name="genes_var" argument="--genes-varmodeling" type="integer" value="1000" label="Number of genes for mean-variance modeling" help="Default: 1000" />
-            <param name="permutation" argument="--permutation-round" type="integer" value="10" label="Number of permutations" help="The rounds for permutation. The permutation time is (# genes) * x for x rounds of permutation. Suggested value: 100 (may take longer time). Default: 10" />
+            <param name="permutation" argument="--permutation-round" type="integer" value="2" label="Number of permutations" help="The rounds for permutation. The permutation time is (# genes) * x for x rounds of permutation. Default: 2" />
             <param name="remove_outliers" argument="--remove-outliers" type="boolean" truevalue="--remove-outliers" falsevalue="" checked="false" optional="true" label="Try to remove outliers" help="Turning this option on will slow the algorithm" />
             <param name="adjust_method" argument="--adjust-method" type="select" label="P-Value Adjustment Method" help="Method for sgRNA-level p-value adjustment, including False Discovery Rate (FDR), Holm's method (Holm), or Pounds's method (Pounds). Default: FDR">
                 <option value="fdr" selected="True">FDR</option>
@@ -87,7 +87,7 @@
             <param name="update_eff" argument="--update-efficiency" type="boolean" truevalue="--update-efficiency" falsevalue="" checked="false" optional="true"
                 label="Update efficiency" help="Iteratively update sgRNA efficiency during EM iteration" />
             <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false"
-                label="Output logfile" help="This file includes the logging information during the execution. For count command, it will list some basic statistics of the dataset at the end, including the number of reads, the number of reads mapped to the library, the number of zero-count sgRNAs, etc. Default: No" />
+                label="Output Log file" help="This file includes the logging information during the execution. For count command, it will list some basic statistics of the dataset at the end, including the number of reads, the number of reads mapped to the library, the number of zero-count sgRNAs, etc. Default: No" />
         </section>
     </inputs>
     <outputs>
diff -r eab37e8fea75 -r 93f268840b0c test-data/out.count.bam.txt
--- a/test-data/out.count.bam.txt	Wed Feb 14 06:42:36 2018 -0500
+++ b/test-data/out.count.bam.txt	Sat Feb 17 10:41:41 2018 -0500
@@ -1,4 +1,4 @@
-sgRNA	Gene	sample1
+sgRNA	Gene	test1.bam
 s_10007	CCNA1	0
 s_10008	CCNA1	0
 s_10027	CCNC	0
diff -r eab37e8fea75 -r 93f268840b0c test-data/out.count.fastq.txt
--- a/test-data/out.count.fastq.txt	Wed Feb 14 06:42:36 2018 -0500
+++ b/test-data/out.count.fastq.txt	Sat Feb 17 10:41:41 2018 -0500
@@ -1,4 +1,4 @@
-sgRNA	Gene	sample1
+sgRNA	Gene	test1.fastq.gz
 s_47512	RNF111	1
 s_24835	HCFC1R1	1
 s_14784	CYP4B1	4