comparison mothur/tools/mothur/libshuff.xml @ 2:e990ac8a0f58

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

1:fcc0778f6987

<tool id="mothur_libshuff" name="Libshuff" version="1.16.0">
 <description>Cramer-von Mises tests communities for the same structure</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='libshuff'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.libshuff\.summary$:'$summary,'^\S+\.libshuff\.coverage$:'$coverage
  --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
  #end if
  --READ_group=$group
  #if len($iters.__str__) > 0:
   --iters=$iters
  #end if
  #if $form == "discrete":
   #if 1.0 >= float($form.step.__str__) > 0.0:
    --step=$form.step
   #end if
   #if 1.0 >= float($cutoff.__str__) > 0.0:
    --cutoff=$form.cutoff
   #end if
  #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"/>
   </when>
  </conditional>
  <param name="group" type="data" format="groups" label="read.dist(group=) - Groups"/>
  <!-- ? conditional - to hide complexity -->
  <param name="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
  <conditional name="form">
   <param name="form" type="select" label="form - Select a Clustering Method" help="">
    <option value="integral" selected="true">Integral</option>
    <option value="discrete">Discrete</option>
   </param>

2:e990ac8a0f58

<tool id="mothur_libshuff" name="Libshuff" version="1.19.0">
 <description>Cramer-von Mises tests communities for the same structure</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='libshuff'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.libshuff\.summary$:'$summary,'^\S+\.libshuff\.coverage$:'$coverage
  --outputdir='$logfile.extra_files_path'
  --phylip=$dist
  --group=$group
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
    --groups=$groups
  #end if
  #if len($iters.__str__) > 0:
   --iters=$iters
  #end if
  $sim
  #if $form == "discrete":
   #if 1.0 >= float($form.step.__str__) > 0.0:
    --step=$form.step
   #end if
   #if 1.0 >= float($cutoff.__str__) > 0.0:
    --cutoff=$form.cutoff
   #end if
  #end if
 </command>
 <inputs>
  <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
  <param name="group" type="data" format="groups" label="group - Groups"/>
  <param name="groups" type="select" label="groups - Groups to condider" 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="iters" type="integer" value="10000" label="iters - Number of iterations to try (default 10000)"/>
  <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" help=""/>
  <conditional name="form">
   <param name="form" type="select" label="form - Select a Clustering Method" help="">
    <option value="integral" selected="true">Integral</option>
    <option value="discrete">Discrete</option>
   </param>