# HG changeset patch
# User iuc
# Date 1575586838 18000
# Node ID 9ccec6ed8e82b91a8ddaecd03602a44adeafaecc
# Parent  6e094623868865309d3963a36ff5050e1e09715e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit a82e4981dac025c909244acd7127c215bdb519a7"

diff -r 6e0946238688 -r 9ccec6ed8e82 README.md
--- a/README.md	Fri Nov 08 18:49:57 2019 -0500
+++ b/README.md	Thu Dec 05 18:00:38 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 6e0946238688 -r 9ccec6ed8e82 dada2_makeSequenceTable.xml
--- a/dada2_makeSequenceTable.xml	Fri Nov 08 18:49:57 2019 -0500
+++ b/dada2_makeSequenceTable.xml	Thu Dec 05 18:00:38 2019 -0500
@@ -15,7 +15,7 @@
 @WRITE_FOO@
 
 library(dada2, quietly=T)
-#if $plot == "yes"
+#if $plot
 library(ggplot2, quietly=T)
 #end if
 
@@ -29,7 +29,7 @@
 reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
 df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
 
-#if $plot == "yes"
+#if $plot
 pdf( '$plot_output' )
 ggplot(data=df, aes(x=length, y=count)) +
     geom_col() +
@@ -75,8 +75,8 @@
     <tests>
         <test expect_num_outputs="2">
             <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
-            <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2"/>
-            <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" />
+			<output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2"/>
+            <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" compare="sim_size" delta="3000" />
         </test>
         <test expect_num_outputs="1">
             <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
diff -r 6e0946238688 -r 9ccec6ed8e82 macros.xml
--- a/macros.xml	Fri Nov 08 18:49:57 2019 -0500
+++ b/macros.xml	Thu Dec 05 18:00:38 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 6e0946238688 -r 9ccec6ed8e82 test-data/complexity.pdf
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