Mercurial > repos > jjohnson > mothur_toolsuite
diff mothur/tools/mothur/trim.seqs.xml @ 4:5265aa9067e0
set output formats to match input formats
author | jjohnson |
---|---|
date | Wed, 08 Jun 2011 15:02:44 -0500 |
parents | e990ac8a0f58 |
children | e2e2071d2c62 |
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--- a/mothur/tools/mothur/trim.seqs.xml Wed Jun 08 14:59:08 2011 -0500 +++ b/mothur/tools/mothur/trim.seqs.xml Wed Jun 08 15:02:44 2011 -0500 @@ -37,7 +37,7 @@ $oligo.allfiles #if $oligo.allfiles.value: --datasetid='$logfile.id' --new_file_path='$__new_file_path__' - --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.groups)$:groups' + --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.groups)$:groups' #end if #end if #if $qual.add == "yes": @@ -95,11 +95,11 @@ <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="fasta" name="trim_fasta" label="${tool.name} on ${on_string}: trim.fasta"/> - <data format="qual" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual"> + <data format_source="qfile" name="trim_qual" label="${tool.name} on ${on_string}: trim.qual"> <filter>(qual['add'] == 'yes' and len(qual['qfile'].__str__) > 0)</filter> </data> - <data format="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/> - <data format="qual" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual"> + <data format_source="fasta" name="scrap_fasta" label="${tool.name} on ${on_string}: scrap.fasta"/> + <data format_source="qfile" name="scrap_qual" label="${tool.name} on ${on_string}: scrap.qual"> <filter>(qual['add'] == 'yes' and len(qual['qfile'].__str__) > 0)</filter> </data> <data format="groups" name="groups_file" label="${tool.name} on ${on_string}: groups">