comparison mothur/tools/mothur/cluster.classic.xml @ 2:e990ac8a0f58

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

1:fcc0778f6987

<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.16.0">
 <description>Assign sequences to OTUs (Dotur implementation)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='cluster.classic'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist
  --outputdir='$logfile.extra_files_path'
  --READ_cmd='read.dist'
  #if $matrix.format == "column":
   --READ_column=$matrix.dist
   --READ_name=$matrix.name
  #elif $matrix.format == "phylip":
   --READ_phylip=$matrix.dist
   #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0:
    --READ_name=$matrix.name
   #end if
  #end if
  $sim
  #if float($cutoff.__str__) > 0.0:
   --READ_cutoff=$cutoff
  #end if
  $hard
  #if len($precision.__str__) > 0:
   --READ_precision=$precision
  #end if
  #if len($method.__str__) > 0:
   --method=$method
  #end if
 </command>
 <inputs>
  <conditional name="matrix">
   <param name="format" type="select" label="Select a Distance Matrix Format" help="">
    <option value="column">Pairwise Column Matrix</option>
    <option value="phylip">Phylip Distance Matrix</option>
   </param>
   <when value="column">
    <param name="dist" type="data" format="pair.dist" label="read.dist(column=) - Distance Matrix"/>
    <param name="name" type="data" format="names" label="read.dist(name=) - Sequences Name reference"/>
   </when>
   <when value="phylip">
    <param name="dist" type="data" format="lower.dist,square.dist" label="read.dist(phylip=) - Distance Matrix"/>
    <param name="name" type="data" format="names" optional="true" label="read.dist(name=) - Sequences Name reference"/>
   </when>
  </conditional>
  <!-- ? conditional - to hide complexity -->
  <param name="method" type="select" label="method - Select a Clustering Method" help="">
   <option value="furthest" selected="true">Furthest neighbor</option>
   <option value="nearest">Nearest neighbor</option>
   <option value="average">Average neighbor</option>
   <option value="weighted">Weighted</option>
  </param>
  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
                 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
  <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding" 
                 help=""/>
  <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
                 help="Set higher precision for longer genome scale sequence lengths">
   <option value="10">.1</option>
   <option value="100" selected="true">.01</option>
   <option value="1000">.001</option>
   <option value="10000">.0001</option>
   <option value="100000">.00001</option>
   <option value="1000000">.000001</option>
  </param>
  <param name="sim" type="boolean" checked="false" truevalue="--READ_sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" 
                 help=""/>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>

2:e990ac8a0f58

<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.19.0">
 <description>Assign sequences to OTUs (Dotur implementation)</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='cluster.classic'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist
  --outputdir='$logfile.extra_files_path'
  --phylip=$dist
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name=$name
  #end if
  #if len($method.__str__) > 0:
   --method=$method
  #end if
  #if float($cutoff.__str__) > 0.0:
   --cutoff=$cutoff
  #end if
  $hard
  #if len($precision.__str__) > 0:
   --precision=$precision
  #end if
  $sim
 </command>
 <inputs>
  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
  <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/>
  <!-- ? conditional - to hide complexity -->
  <param name="method" type="select" label="method - Select a Clustering Method" help="">
   <option value="furthest">Furthest neighbor</option>
   <option value="nearest">Nearest neighbor</option>
   <option value="average" selected="true">Average neighbor</option>
   <option value="weighted">Weighted</option>
  </param>
  <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" 
                 help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
  <param name="hard" type="boolean" checked="true" truevalue="--hard=true" falsevalue="--hard=false" label="hard - Use hard cutoff instead of rounding" 
                 help=""/>
  <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values"
                 help="Set higher precision for longer genome scale sequence lengths">
   <option value="10">.1</option>
   <option value="100" selected="true">.01</option>
   <option value="1000">.001</option>
   <option value="10000">.0001</option>
   <option value="100000">.00001</option>
   <option value="1000000">.000001</option>
  </param>
  <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" 
                 help=""/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
  <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>