diff trimmomatic.xml @ 7:6eeacf19a38e draft

Version 0.36.3: fix the naming of output collections to differentiate btwn paired/unpaired; document the _JAVA_OPTIONS env var (thanks Marius van den Beek).

--- a/trimmomatic.xml	Fri Feb 24 05:12:32 2017 -0500
+++ b/trimmomatic.xml	Tue Mar 21 08:42:05 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.36.2">
+<tool id="trimmomatic" name="Trimmomatic" version="0.36.3">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <macros>
     <import>trimmomatic_macros.xml</import>
@@ -175,12 +175,12 @@
     <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
       <filter>readtype['single_or_paired'] == 'se'</filter>
     </data>
-    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired">
+    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
       <filter>readtype['single_or_paired'] == "collection"</filter>
       <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
       <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
     </collection>
-      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired">
+      <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
         <filter>readtype['single_or_paired'] == "collection"</filter>
         <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
         <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>