comparison mothur/tools/mothur/summary.shared.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_summary_shared" name="Summary.shared" version="1.19.0"  force_history_refresh="True">
 <description>Summary of calculator values for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary

  #end if
  $all
  $distance
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <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>
  <param name="groups" type="select" label="groups - Pairwise comparision groups" 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="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <options from_file="mothur_calculators.loc">

7:7bfe1f843858

<tool id="mothur_summary_shared" name="Summary.shared" version="1.20.0"  force_history_refresh="True">
 <description>Summary of calculator values for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='summary.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$summary

  #end if
  $all
  $distance
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">
   <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>
  <param name="groups" type="select" label="groups - Pairwise comparision groups" 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="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <options from_file="mothur_calculators.loc">