diff dada2_makeSequenceTable.xml @ 5:ec4a183cc713 draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38

--- a/dada2_makeSequenceTable.xml	Mon Apr 29 09:52:30 2019 -0400
+++ b/dada2_makeSequenceTable.xml	Sun May 05 12:37:14 2019 -0400
@@ -11,6 +11,7 @@
     <configfiles>
         <configfile name="dada2_script"><![CDATA[
 @READ_FOO@
+@WRITE_FOO@
 
 library(dada2, quietly=T)
 #if $plot == "yes"
@@ -19,16 +20,11 @@
 
 samples <- list()
 #for $s in $samples:
-    #if $len($samples) == 1
-    samples <- readRDS('$s')
-    #else
     samples[["$s.element_identifier"]] <- readRDS('$s')
-    #end if
 #end for
-## make sequence table
+
 seqtab <- makeSequenceTable(samples, orderBy = "$orderBy")
 
-
 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)
 
@@ -45,14 +41,13 @@
 
 ## filter by seqlengths
 #if $filter_cond.filter_select != "no"
-    seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max)]
+    seqtab <- seqtab[, nchar(colnames(seqtab)) %in% seq($filter_cond.min, $filter_cond.max), drop=F]
 #end if
-
-write.table(seqtab, "$stable", quote=F, sep="\t", row.names = T, col.names = NA)
+write.data( seqtab, '$stable', "dada2_sequencetable" )
     ]]></configfile>
     </configfiles>
     <inputs>
-        <param name="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
+        <param argument="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
         <param argument="orderBy" type="select" label="Column order">
             <option value="abundance">abundance</option>
             <option value="nsamples">nsamples</option>
@@ -77,9 +72,18 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <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" />
+            <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" />
+        </test>
+        <test expect_num_outputs="1">
+            <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/>
+            <param name="filter_cond|filter_select" value="minmax"/>
+            <param name="filter_cond|min" value="200"/>
+            <param name="filter_cond|max" value="300"/>
+            <param name="plot" value="no" />
+            <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" />
         </test>
     </tests>
     <help><![CDATA[