view mothur/tools/mothur/heatmap.sim.xml @ 22:ed906f8149bb

Mothur - html escape amperand in calculator option label

<tool id="mothur_heatmap_sim" name="Heatmap.sim" version="1.23.0"  force_history_refresh="True">
 <description>Generate a heatmap for pariwise similarity</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='heatmap.sim'
  --outputdir='$logfile.extra_files_path'
  #if $as_datasets.__str__ == "yes":
   #if $input.source == 'shared':
    --result='^mothur.\S+\.logfile$:'$logfile
    --datasetid='$logfile.id' --new_file_path='$__new_file_path__'
    --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.heatmap\.sim\.svg)$:svg'
   #else:
    --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.heatmap\.sim\.svg$:'$heatmap
   #end if
  #else:
   --result='^mothur.\S+\.logfile$:'$logfile
  #end if
  #if $input.source == 'shared':
   --shared=$input.otu
   #if $input.label.__str__ != "None" and len($input.label.__str__) > 0:
    --label='$input.label'
   #end if
   #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0:
    --groups=$input.groups
   #end if
   #if $input.calc.__str__ != "None" and len($input.calc.__str__) > 0:
     --calc='$input.calc'
   #end if
  #elif $input.source == 'column':
   --column=$input.dist
   --name=$input.name
  #elif $input.source == 'phylip':
   --phylip=$input.dist
  #end if
  #if 100 > $fontsize > 0:
   --fontsize=$fontsize
  #end if
 </command>
 <inputs>
  <conditional name="input">
   <param name="source" type="select" label="Generate Heatmap for">
    <option value="shared">shared - Sample Similarity - OTU Shared</option>
    <option value="phylip">phylip - Phylip Distance Matrix</option>
    <option value="column">colomn - Pairwise Column Distance Matrix</option>
   </param>
   <when value="shared">
    <param name="otu" type="data" format="shared" label="shared - OTU Shared"/>
    <param name="label" type="select" label="label - OTU Labels" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="0"/>
       <column name="value" index="0"/>
       <filter type="static_value" name="ignore_header" keep="False" column="0" value = "label"/>
       <filter type="unique_value" name="unq_lbl" column="0" />
      </options>
     </param>
     <param name="groups" type="select" label="groups - Groups to include" multiple="true">
      <options from_dataset="otu">
       <column name="name" index="1"/>
       <column name="value" index="1"/>
       <filter type="static_value" name="ignore_header" keep="False" column="1" value = "Group"/>
       <filter type="unique_value" name="unq_grp" column="1" />
      </options>
     </param>
     <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
      <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
      <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
      <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
      <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
      <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
      <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
      <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
      <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
      <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
      <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
     </param>
   </when>
   <when value="column">
       <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/>
       <param name="name" type="data" format="names" label="name - Names"/>
   </when>
   <when value="phylip">
       <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/>
   </when>
  </conditional>
  <param name="fontsize" type="integer" value="24" label="fontsize - Fontsize (default is 24)"/>
  <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each image"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="svg" name="heatmap" label="${tool.name} on ${on_string}: heatmap.sim.svg">
    <filter>as_datasets != 'true' and input['source'] != 'shared'</filter>
  </data>
 </outputs>
 <requirements>
  <requirement type="binary">mothur</requirement>
 </requirements>
 <tests>
 </tests>
 <help>
**Mothur Overview**

Mothur_, initiated by Dr. Patrick Schloss and his software development team
in the Department of Microbiology and Immunology at The University of Michigan,
provides bioinformatics for the microbial ecology community.

.. _Mothur: http://www.mothur.org/wiki/Main_Page

**Command Documenation**

The heatmap.sim_ command generates a heat map from data provided in either a shared_ file, a phylip_ distance matrix, or a column_ distance matrix and a name_ file.  For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _shared: http://www.mothur.org/wiki/Shared_file
.. _phylip: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _column: http://www.mothur.org/wiki/Column-formatted_distance_matrix
.. _name: http://www.mothur.org/wiki/Name_file
.. _heatmap.sim: http://www.mothur.org/wiki/Heatmap.sim

 </help>
</tool>