Mercurial > repos > pjbriggs > trimmomatic
diff trimmomatic.xml @ 8:a923b799c77c 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).
| author | pjbriggs |
|---|---|
| date | Tue, 21 Mar 2017 08:31:44 -0400 |
| parents | 77dd0fe954c5 |
| children | a775e9fda0ca |
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--- a/trimmomatic.xml Fri Feb 24 04:57:13 2017 -0500 +++ b/trimmomatic.xml Tue Mar 21 08:31:44 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']"/>