comparison 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

6:ce6e81622c6a

<tool id="mothur_collect_single" name="Collect.single" version="1.19.0" 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 isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
   --shared=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):

  <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
  <param name="size" type="integer" value="0" label="size - sample size for OTU prediction (ignored if &lt; 1)" 
    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"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </outputs>
 <requirements>

7:7bfe1f843858

<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'
  #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, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__):
   --rabund=$otu
  #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__):

  <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs (default 10)"/>
  <param name="size" type="integer" value="0" label="size - sample size for OTU prediction (ignored if &lt; 1)" 
    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" />
 </outputs>
 <requirements>