comparison mothur/tools/mothur/remove.rare.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_remove_rare" name="Remove.rare" version="1.19.0">
 <description>Remove rare OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.groups   {list_file_name}.pick.{format} 
  #import re, os.path

    <param name="otu" type="data" format="shared" label="shared - Otu dataset"/>
    <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
     <options from_dataset="otu">
      <column name="name" index="1"/>
      <column name="value" index="1"/>
      <filter type="unique_value" name="unq_grp" column="1" />
     </options>
    </param>
    <param name="bygroup" type="boolean" truevalue="--bygroup=true" falsevalue="" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/> 
    <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels" >
     <options from_dataset="otu">
      <column name="name" index="0"/>
      <column name="value" index="0"/>
      <filter type="unique_value" name="unq_lbl" column="0" />
     </options>
    </param>
   </when>
   <when value="list">

7:7bfe1f843858

<tool id="mothur_remove_rare" name="Remove.rare" version="1.20.0">
 <description>Remove rare OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.groups   {list_file_name}.pick.{format} 
  #import re, os.path

    <param name="otu" type="data" format="shared" label="shared - Otu dataset"/>
    <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
     <options from_dataset="otu">
      <column name="name" index="1"/>
      <column name="value" index="1"/>
      <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
      <filter type="unique_value" name="unq_grp" column="1" />
     </options>
    </param>
    <param name="bygroup" type="boolean" truevalue="--bygroup=true" falsevalue="" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/> 
    <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels" >
     <options from_dataset="otu">
      <column name="name" index="0"/>
      <column name="value" index="0"/>
      <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
      <filter type="unique_value" name="unq_lbl" column="0" />
     </options>
    </param>
   </when>
   <when value="list">