comparison mothur/tools/mothur/unifrac.weighted.xml @ 2:e990ac8a0f58

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

1:fcc0778f6987

<tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.16.0">
 <description>Describes whether two or more communities have the same structure</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='unifrac.weighted'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.wsummary$:'$summary,'^\S+\.weighted\.(column\.|philip\.)?dist$:'$dist
  --outputdir='$logfile.extra_files_path'
  --READ_cmd='read.tree'
  --READ_tree=$tree
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --READ_group='$group'
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups='$groups'
  #end if
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --READ_name='$name'
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  $random
  #if $distance.__str__ != "false":
   --distance=$distance
  #end if
  --processors=2
 </command>
 <inputs>
  <!-- list,group  or shared -->
  <param name="tree" type="data" format="tre" label="read.tree(tree=) - Tree"/>
  <param name="group" type="data" format="groups" label="read.tree(group=) - Group file for the tree"/>
  <param name="groups" type="select" label="groups - Groups to display" 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>
  <param name="name" type="data" format="names" optional="true" label="name - Names file for the tree"/>
  <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
  <param name="random" type="boolean" truevalue="--random=true" falsevalue="" checked="false" label="random - Compare your trees with randomly generated trees" />
  <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Add the distance matrix to your history" />
  <param name="distance" type="select" label="distance - Select a distance matrix for your history">
   <option value="false">None</option>
   <option value="lt">Philip Lower Triangle Matrix</option>
   <option value="square">Philip Square Matrix</option>
   <option value="column">Pairwise Distance Matrix</option>
  </param>
  <!-- random uses input prompts, not sure how to model that
  <param name="random" type="text" value="" label="random - The root name for random tests"/>
  -->
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary">
  </data>
  <data format="lower.dist" name="dist" label="${tool.name} on ${on_string}: dist">
   <filter>distance != 'false'</filter>
   <change_format>
    <when input="distance" value="square" format="square.dist" />

2:e990ac8a0f58

<tool id="mothur_unifrac_weighted" name="unifrac.weighted" version="1.19.0">
 <description>Describes whether two or more communities have the same structure</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='unifrac.weighted'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.wsummary$:'$summary,'^\S+\.weighted\.(column\.|phylip\.)?dist$:'$dist,'^\S+\.weighted$:'$weighted
  --outputdir='$logfile.extra_files_path'
  --tree=$tree
  #if $group.__str__ != "None" and len($group.__str__) > 0:
   --group='$group'
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups='$groups'
  #end if
  #if $name.__str__ != "None" and len($name.__str__) > 0:
   --name='$name'
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  $random
  #if $distance.__str__ != "false":
   --distance=$distance
  #end if
  $root
  --processors=2
 </command>
 <inputs>
  <param name="tree" type="data" format="tre" label="tree - Tree"/>
  <param name="group" type="data" format="groups" label="group - Group file for the tree"/>
  <param name="groups" type="select" label="groups - Select groups for pairwise comparisons" multiple="true">
   <help></help>
   <options from_dataset="group">
    <column name="name" index="1"/>
    <column name="value" index="1"/>
    <filter type="unique_value" name="unq_grp" column="1" />
   </options>
  </param>
  <param name="name" type="data" format="names" optional="true" label="name - Names file for the tree"/>
  <param name="iters" type="integer" value="1000" label="iters - Number of iterations to try (default 1000)"/>
  <param name="random" type="boolean" truevalue="--random=true" falsevalue="" checked="false" label="random - Compare your trees with randomly generated trees" />
  <param name="distance" type="boolean" truevalue="--distance=true" falsevalue="" checked="false" label="distance - Add the distance matrix to your history" />
  <param name="distance" type="select" label="distance - Create a distance matrix for your history">
   <option value="false">None</option>
   <option value="lt">Phylip Lower Triangle Matrix</option>
   <option value="square">Phylip Square Matrix</option>
   <option value="column">Pairwise Distance Matrix</option>
  </param>
  <param name="root" type="boolean" truevalue="--root=true" falsevalue="" checked="false" label="root - the entire root in your calculations" />
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="summary" label="${tool.name} on ${on_string}: summary">
  </data>
  <data format="tabular" name="weighted" label="${tool.name} on ${on_string}: weighted">
   <filter>(random == True)</filter>
  </data>
  <data format="lower.dist" name="dist" label="${tool.name} on ${on_string}: dist">
   <filter>distance != 'false'</filter>
   <change_format>
    <when input="distance" value="square" format="square.dist" />