--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dada2_makeSequenceTable.xml	Fri Mar 08 06:42:56 2019 -0500
@@ -0,0 +1,75 @@
+<tool id="dada2_makeSequenceTable" name="dada2: makeSequenceTable" version="@DADA2_VERSION@">
+    <description>construct a sequence table (analogous to OTU table)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+    Rscript '$dada2_script'
+    ]]></command>
+    <configfiles>
+        <configfile name="dada2_script"><![CDATA[
+@READ_FOO@
+
+library(dada2, quietly=T)
+#if $filter.plot == "yes"
+library(ggplot2, quietly=T)
+#end if
+
+samples <- list()
+#for $s in $samples:
+    #if $len($samples) == 1
+    samples <- $read_data($s)
+    #else
+    samples[["$s.element_identifier"]] <- $read_data($s)
+    #end if
+#end for
+## make sequence table
+seqtab <- makeSequenceTable(samples, orderBy = "$orderby")
+
+## get and plot length distribution
+seqlen <- data.frame(length = nchar(getSequences(seqtab)))
+seqlenq <- quantile(seqlen\$length, probs=c( $filter.plower, $filter.pupper  ))
+
+#if $filter.plot == "yes"
+pdf( '$plot' )
+ggplot(seqlen) + 
+    geom_histogram( aes(x=length), binwidth=1 ) + 
+    geom_vline(xintercept=c(seqlenq[1]-0.5, seqlenq[2]+0.5))
+bequiet <- dev.off()
+#end if
+
+## filter by seqlengths
+#if $filter.filter == "yes"
+seqtab <- seqtab[,nchar(colnames(seqtab)) %in% seqlenq]
+#end if
+
+write.table(seqtab, "$stable", quote=F, sep="\t", row.names = T, col.names = NA)
+    ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
+        <param name="orderby" type="select" label="Column order">
+            <option value="abundance">abundance</option>
+            <option value="nsamples">nsamples</option>
+        </param>
+        <section name="filter" title="Plot and filter sequence lengths">
+            <param name="plower" type="float" min="0" max="1" value="0.01" label="lower quantile" />
+            <param name="pupper" type="float" min="0" max="1" value="0.99" label="upper quantile" />
+            <param name="plot" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="plot sequence length distribution" />
+            <param name="filter" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="filter sequence length using quantiles" />
+	</section>
+    </inputs>
+    <outputs>
+        <data name="stable" format="dada2_sequencetable" label="${tool.name} on ${on_string}"/>
+        <data name="plot" format="pdf" label="${tool.name} on ${on_string}: sequence length distribution">
+            <filter>filter['plot']</filter>
+	</data>
+    </outputs>
+
+    <help><![CDATA[
+        TODO: Fill in help.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>