comparison mothur/tools/mothur/remove.rare.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

34:1be61ceb20d7

  #end if
  #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
   --label=$input.label
  #end if
  --nseqs=$nseqs
  --result=#echo ','.join($results)
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Select Input Format">
    <option value="shared">shared</option>

     <options>
      <filter type="data_meta" ref="otu" key="labels" />
     </options>
    </param>
   </when>
  </conditional>
  <param name="nseqs" type="integer" value="1" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> 
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="otu" name="pick_otu" label="${tool.name} on ${on_string}: pick.${input.otu.ext}"/>
  <data format="groups" name="pick_group" label="${tool.name} on ${on_string}: pick.groups">
   <filter>input['source'] == 'list'</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

35:95d75b35e4d2

  #end if
  #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
   --label=$input.label
  #end if
  --nseqs=$nseqs
	--result=#echo ','.join($results)
  #if $count.__str__ != "None" and len($count.__str__) > 0:
    --count=$count
   #end if
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Select Input Format">
    <option value="shared">shared</option>

     <options>
      <filter type="data_meta" ref="otu" key="labels" />
     </options>
    </param>
   </when>
 </conditional>
 <param name = "count" type = "data" format = "count_table" optional = "true" label="count" help ="If you clustered with a count file, be sure to include it"/>
  <param name="nseqs" type="integer" value="1" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> 
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format_source="otu" name="pick_otu" label="${tool.name} on ${on_string}: pick.${input.otu.ext}"/>
  <data format="groups" name="pick_group" label="${tool.name} on ${on_string}: pick.groups">
   <filter>input['source'] == 'list'</filter>
  </data>
 </outputs>
 <requirements>
<requirement type = "package" version ="1.33">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**