comparison mothur/tools/mothur/get.group.xml @ 2:e076d95dbdb5

Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository

1:c7923b34dea4

<tool id="mothur_get_group" name="Get.group" version="1.16.0">
 <description>group names from shared or from list and group</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='get.group'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.bootGroups$:'$bootgroups
  --outputdir='$logfile.extra_files_path'
  --READ_cmd='read.otu'
  #if $input.source == 'similarity':
   --READ_list=$input.otu
   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
    --READ_group='$otu_group'
   #end if
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --READ_groups='$input.groups'
   #end if
  #elif $input.source == 'shared':
   --READ_shared=$input.otu
   #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0:
    --READ_group='$otu_group'
   #end if
  #end if
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Generate principle components for">
    <option value="similarity">OTU list</option>
    <option value="shared">OTU Shared</option>
   </param>
   <when value="similarity">
     <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/>
     <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="otu_group">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
   <when value="shared">
     <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/>
     <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
   </when>
  </conditional>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="groups" name="bootgroups" label="${tool.name} on ${on_string}: bootGroups" />
 </outputs>

2:e076d95dbdb5

<tool id="mothur_get_group" name="Get.group" version="1.19.0">
 <description>group names from shared or from list and group</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='get.group'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.bootGroups$:'$bootgroups
  --outputdir='$logfile.extra_files_path'
  --shared=$otu
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="groups" name="bootgroups" label="${tool.name} on ${on_string}: bootGroups" />
 </outputs>