annotate mothur/tools/mothur/split.abund.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

<tool id="mothur_split_abund" name="Split.abund" version="1.20.0" force_history_refresh="True">
 <description>Separate sequences into rare and abundant groups</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='split.abund'
  #import re, os.path
  --result='^mothur.\S+\.logfile$:'$logfile
  ## --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.abund\.list$:'$abund_list,'^\S+\.rare\.list$:'$rare_list,'^\S+\.rare\.accnos$:'$rare_accnos,'^\S+\.abund\.accnos$:'$abund_accnos
  --outputdir='$logfile.extra_files_path'
  #set datasets = []
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.fasta)$:${fasta.ext}','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.groups)$:groups','^\S+?\.((unique|[0-9.]+)\.(rare|abund)\.accnos)$:accnos'
  #end if
  --fasta=$fasta
  #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.fasta)$',$os.path.basename($fasta.__str__)) + ":" + $fasta.ext + "'"]
  #if $search.type == "list":
   --list=$search.input
   #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.list)$',$os.path.basename($search.input.__str__)) + ":list'"]
   #if $accnos:
     #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.accnos)$',$os.path.basename($search.input.__str__)) + ":accnos'"]
   #end if
   #if $search.label.__str__ != "None" and len($search.label.__str__) > 0:
    --label=$search.label
   #end if
  #elif $search.type == "name":
   --name=$search.input
   #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.names)$',$os.path.basename($search.input.__str__)) + ":names'"]
   #if $accnos:
     #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.accnos)$',$os.path.basename($search.input.__str__)) + ":accnos'"]
   #end if
  #end if
  --cutoff=$cutoff
  #if $split.type == 'yes':
   #if $split.group.__str__ != "None" and len($split.group.__str__) > 0:
    --group=$split.group
    #set datasets = $datasets + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'^\1.(.*\.groups)$',$os.path.basename($split.group.__str__)) + ":groups'"]
   #end if
   #if $split.groups.__str__ != "None" and len($split.groups.__str__) > 0:
    --groups=$split.groups
   #end if
  #end if
  $accnos
  #if $as_datasets.__str__ == "yes":
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets=#echo ','.join($datasets)
  #end if
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/>
  <conditional name="search">
   <param name="type" type="select" label="Type to screen" help="">
    <option value="list">OTU List</option>
    <option value="name">Name reference</option>
   </param>
   <when value="name">
    <param name="input" type="data" format="names" label="name - Name reference"/>
   </when>
   <when value="list">
    <param name="input" type="data" format="list" label="list - OTU List"/>
    <param name="label" type="select" label="label - OTU Labels" multiple="true" help="Select OTU Labels to filter out all but selected labels">
     <options from_dataset="input">
      <column name="name" index="0"/>
      <column name="value" index="0"/>
     </options>
    </param>
   </when>
  </conditional> <!-- search -->
  <param name="cutoff" type="integer" value="10" label="cutoff - Cutoff parameter is used to qualify what is abundant and rare."/>
  <conditional name="split">
   <param name="type" type="select" label="Parse a group file into abundant and rare groups?" help="">
    <option value="no" selected="true">No</option>
    <option value="yes">Yes</option>
   </param>
   <when value="no"/>
   <when value="yes">
    <param name="group" type="data" format="groups" label="group - Group dataset"/>
    <param name="groups" type="select" label="groups - Group Selection (all used if none are selected)" multiple="true">
     <options from_dataset="group">
      <column name="name" index="1"/>
      <column name="value" index="1"/>
      <filter type="unique_value" name="unq_grp" column="1" />
     </options>
    </param>
   </when>
  </conditional> <!-- split -->
  <param name="accnos" type="boolean" truevalue="--accnos=true" falsevalue="" checked="false" label="accnos - Produce rare and abundant Accession outputs"/>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each label"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <!--
  <data format="list" name="abund_list" label="${tool.name} on ${on_string}: abund.list" />
  <data format="list" name="rare_list" label="${tool.name} on ${on_string}: rare.list" />
  <data format="accnos" name="rare_accnos" label="${tool.name} on ${on_string}: rare.accnos">
   <filter>accnos == True</filter>
  </data>
  <data format="accnos" name="abund_accnos" label="${tool.name} on ${on_string}: abund.accnos">
   <filter>accnos == True</filter>
  </data>
  -->
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The split.abund_ command reads a fasta file and a list_ or a name_ file and splits the sequences into rare and abundant groups.

.. _list: http://www.mothur.org/wiki/List_file
.. _name: http://www.mothur.org/wiki/Name_file
.. _split.abund: http://www.mothur.org/wiki/Split.abund

 </help>
</tool>