# HG changeset patch
# User matthias
# Date 1558977818 14400
# Node ID e09edc2b553ac0d6ae540a92997370d0196ffdf0
# Parent  e9d1e654cc9db11f7a780a35ce6ad3bbeef795cf
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 977f22125c9ad5c3c5560de8946017305c5633c1

diff -r e9d1e654cc9d -r e09edc2b553a dada2_filterAndTrim.xml
--- a/dada2_filterAndTrim.xml	Mon May 27 05:34:36 2019 -0400
+++ b/dada2_filterAndTrim.xml	Mon May 27 13:23:38 2019 -0400
@@ -119,7 +119,7 @@
         <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" structured_like="paired_reads" inherit_format="true">
+        <collection name="paired_output" type="paired" format_source="paired_reads">
             <filter>paired_cond['paired_select'] == "paired"</filter>
         </collection>
         <data name="output_single" format_source="reads" >
@@ -138,7 +138,7 @@
     <tests>
         <!-- paired data 
              currently removed `expect_num_outputs="2"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
-        <test>
+        <test expect_num_outputs="3">
             <conditional name="paired_cond">
                 <param name="paired_select" value="paired"/>
                 <param name="paired_reads">
@@ -155,7 +155,7 @@
             <output name="outtab" value="filterAndTrim_F3D0.tab" ftype="tabular"/>
         </test>
         <!-- separate paired data -->
-        <test>
+        <test expect_num_outputs="3">
             <conditional name="paired_cond">
                 <param name="paired_select" value="separate"/>
                 <param name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/>
@@ -203,8 +203,8 @@
         </test>
         <!-- paired data w separate filters and trimmers for reverse 
              currently removed `expect_num_outputs="1"` because of https://github.com/galaxyproject/galaxy/pull/7894-->
-            <test>
-            <conditional name="paired_cond">
+        <test expect_num_outputs="2">
+            <conditional name="paired_cond" >
                 <param name="paired_select" value="paired"/>
                 <param name="paired_reads">
                     <collection type="paired">
diff -r e9d1e654cc9d -r e09edc2b553a macros.xml
--- a/macros.xml	Mon May 27 05:34:36 2019 -0400
+++ b/macros.xml	Mon May 27 13:23:38 2019 -0400
@@ -69,7 +69,7 @@
             <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"/>
-            <param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded."/>
+			<param argument="truncLen" type="integer" value="0" min="0" label="Truncate read length" help="Truncate reads after this amount of bases. Reads shorter than this are discarded. (default 0: no truncation)"/>
         </section>
     </xml>
     <xml name="filters">
diff -r e9d1e654cc9d -r e09edc2b553a test-data/qualityProfileMultiple_rev.pdf
diff -r e9d1e654cc9d -r e09edc2b553a test-data/qualityProfile_rev.pdf