Mercurial > repos > pjbriggs > trimmomatic

comparison trimmomatic.xml @ 7:6eeacf19a38e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 08:42:05 -0400
parents 141bba0e9a77
children 415a165d92bb
comparison
equal deleted inserted replaced
6:141bba0e9a77 7:6eeacf19a38e
1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.2"> 1 <tool id="trimmomatic" name="Trimmomatic" version="0.36.3">
2 <description>flexible read trimming tool for Illumina NGS data</description> 2 <description>flexible read trimming tool for Illumina NGS data</description>
3 <macros> 3 <macros>
4 <import>trimmomatic_macros.xml</import> 4 <import>trimmomatic_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
173 <filter>readtype['single_or_paired'] == "pair_of_files"</filter> 173 <filter>readtype['single_or_paired'] == "pair_of_files"</filter>
174 </data> 174 </data>
175 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in"> 175 <data name="fastq_out" label="${tool.name} on ${readtype.fastq_in.name}" format_source="fastq_in">
176 <filter>readtype['single_or_paired'] == 'se'</filter> 176 <filter>readtype['single_or_paired'] == 'se'</filter>
177 </data> 177 </data>
178 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: paired"> 178 <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${on_string}: paired">
179 <filter>readtype['single_or_paired'] == "collection"</filter> 179 <filter>readtype['single_or_paired'] == "collection"</filter>
180 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/> 180 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 paired)" format_source="fastq_pair['forward']"/>
181 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/> 181 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 paired)" format_source="fastq_pair['reverse']"/>
182 </collection> 182 </collection>
183 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${readtype.fastq_pair.name}: unpaired"> 183 <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${on_string}: unpaired">
184 <filter>readtype['single_or_paired'] == "collection"</filter> 184 <filter>readtype['single_or_paired'] == "collection"</filter>
185 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/> 185 <data name="forward" label="${tool.name} on ${readtype.fastq_pair.forward.name} (R1 unpaired)" format_source="fastq_pair['forward']"/>
186 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/> 186 <data name="reverse" label="${tool.name} on ${readtype.fastq_pair.reverse.name} (R2 unpaired)" format_source="fastq_pair['reverse']"/>
187 </collection> 187 </collection>
188 188