# HG changeset patch
# User iuc
# Date 1464690279 14400
# Node ID d856341e03c8375af71394b120f75792435dab07
# Parent  0fb62f07f8b73aff74e1c2a31d8b5844415b91eb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit dd85747b08272b72c7161de9b18d19598bb49de1

diff -r 0fb62f07f8b7 -r d856341e03c8 deseq2.xml
--- a/deseq2.xml	Wed Dec 02 17:41:10 2015 -0500
+++ b/deseq2.xml	Tue May 31 06:24:39 2016 -0400
@@ -52,6 +52,9 @@
             #if $outlier_filter_off:
                 -b
             #end if
+            #if $auto_mean_filter_off:
+                -c
+            #end if
             #if $many_contrasts:
                 -m
             #end if
@@ -59,7 +62,7 @@
     </command>
     <inputs>
         <repeat name="rep_factorName" title="Factor" min="1">
-            <param name="factorName" type="text" value="FactorName" label="Specify a factor name" 
+            <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
                 help="Only letters, numbers and underscores will be retained in this field">
                 <sanitizer>
                     <valid initial="string.letters,string.digits"><add value="_" /></valid>
@@ -105,7 +108,7 @@
         </data>
         <collection name="split_output" type="list" label="DESeq2 result files on ${on_string}">
             <filter>many_contrasts is True</filter>
-            <discover_datasets pattern="vs" visible="true"/>
+            <discover_datasets pattern="None.(?P&lt;designation&gt;.+_vs_.+)" format="tabular" directory="." visible="false"/>
         </collection>
         <data format="pdf" name="plots" label="DESeq2 plots on ${on_string}">
             <filter>pdf == True</filter>
@@ -133,7 +136,7 @@
 <![CDATA[
 .. class:: infomark
 
-**What it does** 
+**What it does**
 
 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution
 
@@ -145,7 +148,7 @@
 The following table gives some examples of factors and their levels:
 
 ========= ============== ===============
-Factor    Factor level 1 Factor level 2 
+Factor    Factor level 1 Factor level 2
 --------- -------------- ---------------
 Treatment Treated        Untreated
 --------- -------------- ---------------
diff -r 0fb62f07f8b7 -r d856341e03c8 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 02 17:41:10 2015 -0500
+++ b/tool_dependencies.xml	Tue May 31 06:24:39 2016 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="deseq2" version="1.8.2">
-       <repository changeset_revision="acbeda52bf87" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+       <repository changeset_revision="81a3e281bf21" name="package_deseq2_1_8_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>