diff macros.xml @ 7:75403243703a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit c2f6071f729b74540354f4a9e7084c9ac468a135

--- a/macros.xml	Fri Jun 30 07:59:02 2023 +0000
+++ b/macros.xml	Mon Aug 07 01:33:05 2023 +0000
@@ -12,8 +12,8 @@
             <xref type="bioconductor">dada2</xref>
         </xrefs>
     </xml>
-    <token name="@DADA2_VERSION@">1.20</token>
-    <token name="@WRAPPER_VERSION@">1</token>
+    <token name="@DADA2_VERSION@">1.28</token>
+    <token name="@WRAPPER_VERSION@">0</token>
 
     <xml name="version_command">
         <version_command><![CDATA[
@@ -43,17 +43,18 @@
          - uniques is a named integer vector (columns=ASVs, only one rows)-->
     <token name="@READ_FOO@"><![CDATA[
     read.uniques <- function ( fname ) {
-         p <- read.table(fname, header=F, sep="\t")
+         x <- read.table(fname, header=F, sep="\t")
          n <-x[,2]
          names(n)<-x[,1]
+         return(n)
     }
     #def read_data($dataset)
         #if $dataset.is_of_type('dada2_sequencetable')
-            t(as.matrix( read.table('$dataset', header=T, sep="\t", row.names=1) ))
+            t(read.table('$dataset', header=T, sep="\t", row.names=1, check.names=FALSE))
         #else if $dataset.is_of_type('dada2_uniques')
             read.uniques('$dataset')
         #else if $dataset.is_of_type('tabular')
-            read.table('$dataset', header=T, sep="\t", row.names=1)
+            read.table('$dataset', header=T, sep="\t", row.names=1, check.names=FALSE)
         #else
             readRDS('$dataset')
         #end if
@@ -97,7 +98,7 @@
 
     <!-- for filterAndTrim -->
     <xml name="trimmers">
-        <section name="trim" title="Trimming parameters">
+        <section name="trim" title="Trimming parameters" expanded="true">
             <param argument="truncQ" type="integer" value="2" min="0" label="Truncate reads at quality threshold" help="Truncate reads at the first instance of a quality score less than or equal to this threshold"/>
             <param argument="trimLeft" type="integer" value="0" min="0" label="Trim start of each read" help="The number of nucleotides to remove from the start of each read."/>
             <param argument="trimRight" type="integer" value="0" min="0" label="Trim end of each read" help="The number of nucleotides to remove from the end of each read"/>
@@ -105,7 +106,7 @@
         </section>
     </xml>
     <xml name="filters">
-        <section name="filter" title="Filtering parameters">
+        <section name="filter" title="Filtering parameters" expanded="true">
             <param argument="maxLen" type="integer" value="" optional="true" min="0" label="Remove long reads" help="Remove reads with length greater than this value. Default: no length threshold"/>
             <param argument="minLen" type="integer" value="20" min="0" label="Remove short reads" help="Remove reads with length less than this value. Default: 20"/>
             <param argument="maxN" type="integer" value="0" min="0" label="Remove reads with more Ns" help="Note that some of the subsequent dada pipeline steps do not allow Ns"/>