# HG changeset patch
# User iuc
# Date 1575586797 18000
# Node ID 7f8f0e9fcb37e2cb7d9b98015b7ed1de59eb201a
# Parent  1937c2b4da7a05a30c27bf45c4ed85c80ef70369
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"

diff -r 1937c2b4da7a -r 7f8f0e9fcb37 README.md
--- a/README.md	Fri Nov 08 18:49:03 2019 -0500
+++ b/README.md	Thu Dec 05 17:59:57 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 1937c2b4da7a -r 7f8f0e9fcb37 dada2_removeBimeraDenovo.xml
--- a/dada2_removeBimeraDenovo.xml	Fri Nov 08 18:49:03 2019 -0500
+++ b/dada2_removeBimeraDenovo.xml	Thu Dec 05 17:59:57 2019 -0500
@@ -77,7 +77,7 @@
         <test expect_num_outputs="1">
             <param name="unqs" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
             <param name="method" value="pooled"/>
-            <output name="stable_mergepairs" value="removeBimeraDenovo_F3D0_mergepairs.Rdata" ftype="dada2_mergepairs" />
+            <output name="stable_mergepairs" value="removeBimeraDenovo_F3D0_mergepairs.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400"/>
         </test>
     </tests>
     <help><![CDATA[
diff -r 1937c2b4da7a -r 7f8f0e9fcb37 macros.xml
--- a/macros.xml	Fri Nov 08 18:49:03 2019 -0500
+++ b/macros.xml	Thu Dec 05 17:59:57 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 1937c2b4da7a -r 7f8f0e9fcb37 test-data/complexity.pdf
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diff -r 1937c2b4da7a -r 7f8f0e9fcb37 test-data/learnErrors_F3D0_R1.pdf
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diff -r 1937c2b4da7a -r 7f8f0e9fcb37 test-data/learnErrors_F3D0_R2.pdf
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diff -r 1937c2b4da7a -r 7f8f0e9fcb37 test-data/makeSequenceTable_F3D0.pdf
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diff -r 1937c2b4da7a -r 7f8f0e9fcb37 test-data/qualityProfile.pdf
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