diff mothur/tools/mothur/trim.seqs.xml @ 4:5265aa9067e0

set output formats to match input formats

--- 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">