annotate mothur/tools/mothur/get.groups.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

<tool id="mothur_get_groups" name="Get.groups" version="1.16.0">
 <description>Select groups</description>
 <command interpreter="python">
  mothur_wrapper.py 
  #import re, os.path
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  ## adds .pick before the last extension to the input file
  #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__]
  --cmd='get.groups'
  --outputdir='$logfile.extra_files_path'
  --group=$group_in
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
  #if $accnos.__str__ != "None" and len($accnos.__str__) > 0:
   --accnos=$accnos
  #end if
  #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0:
   --fasta=$fasta_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__]
  #end if
  #if $name_in.__str__ != "None" and len($name_in.__str__) > 0:
   --name=$name_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__]
  #end if
  #if $list_in.__str__ != "None" and len($list_in.__str__) > 0:
   --list=$list_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__]
  #end if
  #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0:
   --taxonomy=$taxonomy_in
   #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__]
  #end if
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <param name="group_in" type="data" format="groups" label="group - Groups"/>
  <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true">
   <options from_dataset="group_in">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Accession Names"/>
  <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
  <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/>
  <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/>
  <!-- fix format -->
  <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta">
   <filter>fasta_in != None</filter>
  </data>
  <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name">
   <filter>name_in != None</filter>
  </data>
  <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list">
   <filter>list_in != None</filter>
  </data>
  <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy">
   <filter>taxonomy_in != None</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 get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. 

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


 </help>
</tool>