annotate mothur/tools/mothur/get.sharedseqs.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_get_sharedseqs" name="Get.sharedseqs" version="1.20.0" force_history_refresh="True">
 <description>Get shared sequences at each distance from list and group</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  --cmd='get.sharedseqs'
  --result='^mothur.\S+\.logfile$:'$logfile
  --outputdir='$logfile.extra_files_path'
  --list=$list
  --group=$group
  #set datasets = ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.seqs)$:tabular'"]
  #if $label.__str__ != "None" and len($label.__str__) > 0:
   --label='$label'
  #end if
  #if $seqs_from.selection == 'unique':
   #if $seqs_from.groups.__str__ != "None" and len($seqs_from.groups.__str__) > 0:
    --unique=$seqs_from.groups
   #end if
  #elif $seqs_from.selection == 'shared':
   #if $seqs_from.groups.__str__ != "None" and len($seqs_from.groups.__str__) > 0:
    --shared=$seqs_from.groups
   #end if
  #end if
  #if $fasta.__str__ != "None" and len($fasta.__str__) > 0:
   --fasta=$fasta
   #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.shared.fasta)$:" + $fasta.ext + "'"]
  #end if
  #if $output.__str__ != "None" and len($output.__str__) > 0:
   --output=$output
   #set datasets = $datasets + ["'^\S+?\.((unique|[0-9.]*)(\S+)\.accnos)$:accnos'"]
  #end if
  #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="list" type="data" format="list" label="list - OTU List"/>
  <param name="group" type="data" format="groups" label="group - "/>
  <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" 
     help="By default all are included if no selection is made.">
   <options from_dataset="list">
    <column name="name" index="0"/>
    <column name="value" index="0"/>
   </options>
  </param>
  <param name="fasta" type="data" format="fasta" optional="true" label="fasta - Dataset"/>

  <conditional name="seqs_from">
   <param name="selection" type="select" label="Select Groups" help="">
    <option value="all" selected="true">None (use all groups)</option>
    <option value="unique">OTUs that contain ONLY sequences from the selected groups</option>
    <option value="shared">OTUs that contain sequences from the selected groups</option>
   </param>
   <when value="all"/>
   <when value="unique">
    <param name="groups" type="select" label="unique - Group to analyze" 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>
   <when value="shared">
    <param name="groups" type="select" label="shared - Groups to analyze" 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> <!-- seqs_from -->
  
  <param name="output" type="select" label="output - select the output format" help="accnos can be used with get.seqs, list.seqs and remove.seqs">
    <option value="" selected="true">default: (name  group  bin_number)</option>
    <option value="accnos">accnos (name)</option>
  </param>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
 </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 get.sharedseqs_ command takes a list and group file and outputs a *.shared.seqs file for each distance. This is useful for those cases where you might be interested in identifying sequences that are either unique or shared by specific groups, which you could then classify.

.. _get.sharedseqs: http://www.mothur.org/wiki/Get.sharedseqs

 </help>
</tool>