# HG changeset patch
# User iuc
# Date 1575586902 18000
# Node ID b1e55c248f17c988d4643d4628fe51a9756c5739
# Parent  805daed21ef364760bed2b14206df4d967e0d43c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"

diff -r 805daed21ef3 -r b1e55c248f17 README.md
--- a/README.md	Fri Nov 08 18:51:19 2019 -0500
+++ b/README.md	Thu Dec 05 18:01:42 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 805daed21ef3 -r b1e55c248f17 dada2_mergePairs.xml
--- a/dada2_mergePairs.xml	Fri Nov 08 18:51:19 2019 -0500
+++ b/dada2_mergePairs.xml	Thu Dec 05 18:01:42 2019 -0500
@@ -44,7 +44,7 @@
             <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/>
             <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/>
             <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/>
-            <output name="merged" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs" />
+            <output name="merged" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400" />
         </test>
         <!-- test non-default options -->
         <test>
@@ -52,7 +52,7 @@
             <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/>
             <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/>
             <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/>
-            <output name="merged" value="mergePairs_F3D0_nondefault.Rdata" ftype="dada2_mergepairs" />
+            <output name="merged" value="mergePairs_F3D0_nondefault.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="700"/>
             <param name="minOverlap" value="8" />
             <param name="maxMismatch" value="1"/>
             <param name="justConcatenate" value="TRUE" />
diff -r 805daed21ef3 -r b1e55c248f17 macros.xml
--- a/macros.xml	Fri Nov 08 18:51:19 2019 -0500
+++ b/macros.xml	Thu Dec 05 18:01:42 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 805daed21ef3 -r b1e55c248f17 test-data/complexity.pdf
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