diff mothur/tools/mothur/collect.single.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

--- a/mothur/tools/mothur/collect.single.xml	Mon Jun 27 09:34:14 2011 -0500
+++ b/mothur/tools/mothur/collect.single.xml	Mon Jun 27 10:12:25 2011 -0500
@@ -1,12 +1,14 @@
-<tool id="mothur_collect_single" name="Collect.single" version="1.19.0" force_history_refresh="True">
+<tool id="mothur_collect_single" name="Collect.single" version="1.20.0" force_history_refresh="True">
  <description>Generate collector's curves for OTUs</description>
  <command interpreter="python">
   mothur_wrapper.py 
   --cmd='collect.single'
   --result='^mothur.\S+\.logfile$:'$logfile
   --outputdir='$logfile.extra_files_path'
-  --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
-  --new_datasets='^\S+?\.(\S+)$:tabular'
+  #if $as_datasets.__str__ == 'yes':
+   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
+   --new_datasets='^\S+?\.(\S+)$:tabular'
+  #end if
   #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
    --shared=$otu
   #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
@@ -54,6 +56,7 @@
     help="By default these calculators will base the prediction on a sample that is the same size as the initial sampling"/>
   <param name="freq" type="float" value="0.0" label="freq - frequency for output (default is every 100 sequences)" 
     help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
+  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label and calculator"/>
  </inputs>
  <outputs>
   <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />