# HG changeset patch
# User iuc
# Date 1575586777 18000
# Node ID 6b4ddc3b64bd8b865ea0bb4103878146e669ce32
# Parent  ce4aec98949dfadc24ce052658bb3dac2c27c49e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"

diff -r ce4aec98949d -r 6b4ddc3b64bd README.md
--- a/README.md	Fri Nov 08 18:48:34 2019 -0500
+++ b/README.md	Thu Dec 05 17:59:37 2019 -0500
@@ -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 ce4aec98949d -r 6b4ddc3b64bd dada2_dada.xml
--- a/dada2_dada.xml	Fri Nov 08 18:48:34 2019 -0500
+++ b/dada2_dada.xml	Thu Dec 05 17:59:37 2019 -0500
@@ -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 ce4aec98949d -r 6b4ddc3b64bd macros.xml
--- a/macros.xml	Fri Nov 08 18:48:34 2019 -0500
+++ b/macros.xml	Thu Dec 05 17:59:37 2019 -0500
@@ -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 ce4aec98949d -r 6b4ddc3b64bd test-data/complexity.pdf
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