# HG changeset patch
# User iuc
# Date 1518882113 18000
# Node ID 5e2a28bee02dcde43d257f392a77683ef00db1a7
# Parent  b8da4d41aa1dca7f8fb97b487000351f296c1eeb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 2eea865fe331694058922292e5681b96f4f0b4c7

diff -r b8da4d41aa1d -r 5e2a28bee02d mageck_test.xml
--- a/mageck_test.xml	Wed Feb 14 06:42:55 2018 -0500
+++ b/mageck_test.xml	Sat Feb 17 10:41:53 2018 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="mageck_test" name="MAGeCKs test" version="@VERSION@" >
+<tool id="mageck_test" name="MAGeCKs test" version="@VERSION@.1" >
     <description>- given a table of read counts, perform the sgRNA and gene ranking</description>
     <macros>
         <import>mageck_macros.xml</import>
@@ -31,14 +31,21 @@
 --adjust-method $adv.adjust_method
 $adv.var_samples
 --sort-criteria $adv.sort_criteria
+
 --remove-zero $adv.remove_zero
+#if $adv.remove_zero_threshold:
+    --remove-zero-threshold $adv.remove_zero_threshold
+#end if
+
 --gene-lfc-method $adv.lfc_method
 #if $adv.control_sgrna:
     --control-sgrna $adv.control_sgrna
 #end if
+
 #if $adv.cnv_norm:
     --cnv-norm $adv.cnv_norm
 #end if
+
 #if $adv.cell_line:
     --cell-line $adv.cell_line
 #end if
@@ -65,7 +72,7 @@
             <param name="normcounts" argument="--normcounts-to-file" type="boolean" truevalue="--normcounts-to-file" falsevalue="" checked="false" optional="true" label="Output normalized counts file" help="Default: No"  />
             <param name="pdfreport" argument="--pdf-report" type="boolean" truevalue="--pdf-report" falsevalue="" checked="false" optional="true" label="Output PDF report" help="Generate pdf report of the input file. Default: No" />
             <param name="rscriptOpt" type="boolean" truevalue="True" falsevalue="" checked="false" optional="true" label="Output R script" help="Output the R script used to generate the plots in the pdf report. Default: No" />
-            <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false" label="Output logfile" help="This file includes the logging information during the execution. Default: No" />
+            <param name="out_log" type="boolean" truevalue="True" falsevalue="" checked="false" label="Output Log file" help="This file includes the logging information during the execution. Default: No" />
         </section>
 
         <section name="adv" title="Advanced Options">
@@ -84,12 +91,14 @@
         </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" />
         <expand macro="sort_criteria" />
-        <param name="remove_zero" argument="--remove-zero" type="select" help="Whether to remove zero-count sgRNAs in control and/or treatment experiments {none,control,treatment,both}. Default: None (do not remove those zero-count sgRNAs)" >
-            <option value="none" selected="True">None</option>
+        <param name="remove_zero" argument="--remove-zero" type="select" 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>
             <option value="control">Control</option>
             <option value="treatment">Treatment</option>
-            <option value="both">Both</option>
+            <option value="both" selected="True">Both</option>
+            <option value="any">Any</option>
         </param>
+        <param name="remove_zero_threshold" argument="--remove-zero-threshold" type="float" value="0" label="Remove zero Threshold" help="sgRNA normalized count threshold to be considered removed in the --remove-zero option. Default: 0"/>
         <param name="lfc_method" argument="--gene-lfc-method" type="select" label="Gene Log-Fold Change Method." help="Method to calculate gene log fold changes (LFC) from sgRNA LFCs. Available methods include the median/mean of all sgRNAs (median/mean), or the median/mean sgRNAs that are ranked in front of the alpha cutoff in RRA (alphamedian/alphamean), or the sgRNA that has the second strongest LFC (secondbest). In the alphamedian/alphamean case, the number of sgRNAs correspond to the goodsgrna column in the output, and the gene LFC will be set to 0 if no sgRNA is in front of the alpha cutoff. Default: Median. (new since v0.5.5)">
             <option value="median" selected="True">Median</option>
             <option value="alphamedian">Alphamedian</option>
diff -r b8da4d41aa1d -r 5e2a28bee02d test-data/out.count.bam.txt
--- a/test-data/out.count.bam.txt	Wed Feb 14 06:42:55 2018 -0500
+++ b/test-data/out.count.bam.txt	Sat Feb 17 10:41:53 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 b8da4d41aa1d -r 5e2a28bee02d test-data/out.count.fastq.txt
--- a/test-data/out.count.fastq.txt	Wed Feb 14 06:42:55 2018 -0500
+++ b/test-data/out.count.fastq.txt	Sat Feb 17 10:41:53 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