# HG changeset patch
# User iuc
# Date 1575586475 0
# Node ID 27b384992e759dff60eabf56608010fa588691ec
# Parent  93a3cbe143186e902b4d704cd51c7b8b482535d4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"

diff -r 93a3cbe14318 -r 27b384992e75 README.md
--- a/README.md	Fri Nov 08 18:42:22 2019 -0500
+++ b/README.md	Thu Dec 05 22:54:35 2019 +0000
@@ -1,15 +1,21 @@
 Wrappers for the core functionality of the dada2 package https://benjjneb.github.io/dada2/index.html. 
 
+- assignTaxonomyAddspecies
 - filterAndTrim
 - learnErrors
 - dada
 - mergePairs
 - makeSequenceTable
+- plotComplexity
+- plotQualityProfile
 - removeBimeraDenovo
+- seqCounts
 
 Installation
 ============
 
+A conda release >=4.6 is needed so that the bioconductor-dada2 conda environment can be installed correctly.
+
 The dada2 wrappers can be installed via the toolshed. Since they use datatypes that have been introduced with Galaxy release 19.09 they won't work out of the box for older Galaxy releases. 
 In order to run the tools you may either upgrade Galaxy or execute the following two steps: 
 
diff -r 93a3cbe14318 -r 27b384992e75 dada2_dada.xml
--- a/dada2_dada.xml	Fri Nov 08 18:42:22 2019 -0500
+++ b/dada2_dada.xml	Thu Dec 05 22:54:35 2019 +0000
@@ -104,7 +104,7 @@
             <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
             <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" />
             <output_collection name="data_collection" type="list">
-                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada"/>
+                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
         </test>
         <!-- default, batch -->
@@ -112,7 +112,7 @@
             <param name="batch_cond|batch_select" value="yes"/>
             <param name="batch_cond|derep" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastq.gz" />
             <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" />
-            <output name="dada" value="dada_F3D0_R1.Rdata" ftype="dada2_dada" />
+            <output name="dada" value="dada_F3D0_R1.Rdata" ftype="dada2_dada"  compare="sim_size" delta="10000"/>
        </test>
         <!-- test non-default options -->
         <test>
@@ -121,7 +121,7 @@
             <param name="batch_cond|pool" value="pseudo"/>
             <param name="err" value="learnErrors_F3D0_R1.Rdata" ftype="dada2_errorrates" />
             <output_collection name="data_collection" type="list">
-                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada"/>
+                <element name="filterAndTrim_F3D0_R1.fq.gz" file="dada_F3D0_R1.Rdata" ftype="dada2_dada" compare="sim_size" delta="10000"/>
             </output_collection>
         </test>
     </tests>
diff -r 93a3cbe14318 -r 27b384992e75 macros.xml
--- a/macros.xml	Fri Nov 08 18:42:22 2019 -0500
+++ b/macros.xml	Thu Dec 05 22:54:35 2019 +0000
@@ -8,7 +8,7 @@
     </xml>
 
     <token name="@DADA2_VERSION@">1.12</token>
-    <token name="@WRAPPER_VERSION@">0</token>
+    <token name="@WRAPPER_VERSION@">1</token>
 
     <xml name="version_command">
         <version_command><![CDATA[
diff -r 93a3cbe14318 -r 27b384992e75 test-data/complexity.pdf
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