comparison mothur/tools/mothur/rarefaction.shared.xml @ 27:49058b1f8d3f

Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur

26:5c77423823cb

<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.20.0">
 <description>Generate inter-sample rarefaction curves for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='rarefaction.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction

   --label='$label'
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  $jumble
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc='$calc'
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">

  </param>
  <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
   <help>All groups will be analyzed by default if none are selected</help>
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
    <filter type="add_value" name="all" value="all" />
   </options>
  </param>
  <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
  <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
   <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
  </param>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" />
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

27:49058b1f8d3f

<tool id="mothur_rarefaction_shared" name="Rarefaction.shared" version="1.26.0" force_history_refresh="True">
 <description>Generate inter-sample rarefaction curves for OTUs</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='rarefaction.shared'
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.rarefaction$:'$rarefaction

   --label='$label'
  #end if
  #if $groups.__str__ != "None" and len($groups.__str__) > 0:
   --groups=$groups
  #end if
  #if $design.use:
   --design=$design.design
   #if $design.sets.__str__ != '':
    --sets='$design.sets'  
   #end if
  #end if
  #if int($iters.__str__) > 0:
   --iters=$iters
  #end if
  $jumble
  #if $calc.__str__ != "None" and len($calc.__str__) > 0:
    --calc='$calc'
  #end if
  #if $subsample.use.__str__ == 'yes':
   #if $subsample.subsample.__str__ != '':
     --subsample=$subsample.subsample
   #else
     --subsample=T
   #end if
   #if $subsample.subsampleiters.__str__ != '':
     --subsampleiters=$subsample.subsampleiters
   #end if
   --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
   --new_datasets='^\S+?\.ave-std\.((unique|[0-9.]*)(\..*?)+\.shared\.rarefaction)$:tabular'
  #end if
 </command>
 <inputs>
  <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
  <param name="label" type="select" label="label - OTU Labels" multiple="true">

  </param>
  <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
   <help>All groups will be analyzed by default if none are selected</help>
   <options>
    <filter type="data_meta" ref="otu" key="groups" />
    <!--
    <filter type="add_value" name="all" value="all" />
    -->
   </options>
  </param>
  <conditional name="design">
    <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label=" run on a per set basis using a design file"/>
    <when value="yes">
    <param name="design" type="data" format="design" label="design - assigns groups to sets" 
           help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
    <param name="sets" type="select" label="sets - group sets to analyze" multiple="true">
     <options>
      <filter type="data_meta" ref="design" key="groups" />
     </options>
    </param>
    </when>
    <when value="no"/>
  </conditional>

  <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/>
  <param name="jumble" type="boolean" truevalue="" falsevalue="--jumble=false" checked="true" label="jumble"/>
  <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
   <option value="sharedobserved" selected="true">sharedobserved - the number of sequences in two samples</option>
   <option value="sharednseqs">sharednseqs - the number of sequences in two samples</option>
  </param>
  <conditional name="subsample">
    <param name="use" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="produce subsample rarefactions"/>
    <when value="yes">
      <param name="subsample" type="integer" value="" optional="true" label="subsample - size pergroup of the sample" 
             help="Leave blank to use the size of your smallest group"/>
      <param name="subsampleiters" type="integer" value="0" optional="true" label="subsampleiters - Number of times to run the subsample"/>
    </when>
    <when value="no"/>
  </conditional>

 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="tabular" name="rarefaction" label="${tool.name} on ${on_string}: shared.rarefaction" />
 </outputs>
 <requirements>
  <requirement type="package" version="1.27">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**