changeset 8:e9d1e654cc9d draft

planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 7831a1e3225240028b30ae02808bdff9babaf368-dirty

--- a/dada2_filterAndTrim.xml	Wed May 08 03:47:42 2019 -0400
+++ b/dada2_filterAndTrim.xml	Mon May 27 05:34:36 2019 -0400
@@ -53,8 +53,8 @@
 filt.fwd <- NULL
 filt.rev <- NULL
 #if $paired_cond.paired_select == "paired"
-    fwd <- c(fwd, '$paired_cond.reads.forward')
-    rev <- c(rev, '$paired_cond.reads.reverse')
+    fwd <- c(fwd, '$paired_cond.paired_reads.forward')
+    rev <- c(rev, '$paired_cond.paired_reads.reverse')
     filt.fwd <- c(filt.fwd, '$paired_output.forward')
     filt.rev <- c(filt.rev, '$paired_output.reverse')
 #else if $paired_cond.paired_select == "separate"
@@ -75,6 +75,8 @@
 
 #if $paired_cond.paired_select == "separate":
     rownames(ftout) <- c( '$paired_cond.forward.element_identifier' )
+#else if $paired_cond.paired_select == "paired"
+    rownames(ftout) <- c( '$paired_cond.paired_reads.element_identifier' )
 #else:
     rownames(ftout) <- c( '$paired_cond.reads.element_identifier' )
 #end if
@@ -89,14 +91,14 @@
                 <option value="single">single</option>
             </param>
             <when value="paired">
-                <param name="reads" argument="fwd/rev" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Paired short read data"/>
+                <param name="paired_reads" argument="fwd/rev" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired short read data"/>
             </when>
             <when value="separate">
-                <param name="forward" argument="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Forward read data"/>
-                <param name="reverse" argument="rev" type="data" format="fastqsanger,fastqsanger.gz" label="Reverse read data"/>
+                <param name="forward" argument="fwd" type="data" format="fastq,fastq.gz" label="Forward read data"/>
+                <param name="reverse" argument="rev" type="data" format="fastq,fastq.gz" label="Reverse read data"/>
             </when>
             <when value="single">
-                <param name="reads" argument="fwd" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/>
+                <param name="reads" argument="fwd" type="data" format="fastq,fastq.gz" label="Short read data"/>
             </when>
         </conditional>
         <expand macro="trimmers"/>
@@ -113,22 +115,20 @@
             </when>
         </conditional>
         <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" />
-        <param name="orientFwd" argument="orinent.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/>
+        <param name="orientFwd" argument="orient.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/>
         <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" />
     </inputs>
     <outputs>
-        <collection name="paired_output" type="paired">
-            <data name="forward" format="fastqsanger.gz" />
-            <data name="reverse" format="fastqsanger.gz" />
+        <collection name="paired_output" type="paired" structured_like="paired_reads" inherit_format="true">
             <filter>paired_cond['paired_select'] == "paired"</filter>
         </collection>
-        <data name="output_single" format="fastqsanger.gz" >
+        <data name="output_single" format_source="reads" >
             <filter>paired_cond['paired_select'] == "single"</filter>
         </data>
-        <data name="output_fwd" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Forward reads" >
+        <data name="output_fwd" format_source="forward" label="${tool.name} on ${on_string}: Forward reads" >
             <filter>paired_cond['paired_select'] == "separate"</filter>
         </data>
-		<data name="output_rev" format="fastqsanger.gz" label="${tool.name} on ${on_string}: Reverse reads" >
+        <data name="output_rev" format_source="reverse" label="${tool.name} on ${on_string}: Reverse reads" >
             <filter>paired_cond['paired_select'] == "separate"</filter>
         </data>
         <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics">
@@ -141,7 +141,7 @@
         <test>
             <conditional name="paired_cond">
                 <param name="paired_select" value="paired"/>
-                <param name="reads">
+                <param name="paired_reads">
                     <collection type="paired">
                         <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
                         <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>
@@ -206,7 +206,7 @@
             <test>
             <conditional name="paired_cond">
                 <param name="paired_select" value="paired"/>
-                <param name="reads">
+                <param name="paired_reads">
                     <collection type="paired">
                         <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
                         <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/>

--- a/macros.xml	Wed May 08 03:47:42 2019 -0400
+++ b/macros.xml	Mon May 27 05:34:36 2019 -0400
@@ -8,7 +8,7 @@
     </xml>
 
     <token name="@DADA2_VERSION@">1.10.0</token>
-    <token name="@WRAPPER_VERSION@">2</token>
+    <token name="@WRAPPER_VERSION@">3</token>
 
     <xml name="version_command">
         <version_command><![CDATA[