view mothur/tools/mothur/corr.axes.xml @ 7:7bfe1f843858

Support Mothur v1.20 trim.seqs - added name parameter and optional trim.names output phylo.diversity - group optional, put group and groups in conditional - breaks get.lineage remove.lineage - allow multiple taxons dist.shared - added processors consensus.seqs - add cutoff parameter trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs new tools - chimera.uchime deunique.tree count.seqs shared/relabund files - Column headings refactor lib/galaxy/datatypes/metagenomics.py add filters to label and group selects in tool configs mothur_wrapper.py updated with new tools params

<tool id="mothur_corr_axes" name="Corr.axes" version="1.20.0">
 <description>correlation of data to axes</description>
 <command interpreter="python">
  mothur_wrapper.py 
  ## output {group_file_name}.pick.{label}.groups   {list_file_name}.pick.{label}.list 
  #import re, os.path
  --cmd='corr.axes'
  --outputdir='$logfile.extra_files_path'
  #if $input.source == 'shared':
   #if isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__):
    --shared=$input.otu
   #elif isinstance($input.otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('relabund').__class__):
    --relabund=$input.otu
   #end if
   #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=$input.groups
   #end if
  #else:
   --metadata=$input.metadata
  #end if
  --method=$method
  --axes=$axes
  #if int($numaxes.__str__) > 0:
   --numaxes=$numaxes
  #end if
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.corr.axes$:'$corr_axes
 </command>
 <inputs>
  <param name="axes" type="data" format="axes" label="axes - a pcoa axes dataset"/>
  <conditional name="input">
   <param name="source" type="select" label="Generate Collector Curvers for">
    <option value="shared">OTU Shared or Relabund</option>
    <option value="metadata">Metadata table</option>
   </param>
   <when value="shared">
     <param name="otu" type="data" format="shared,relabund" label="shared or relabund - OTU Shared or Relabund"/>
     <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 - Pairwise comparision groups" 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>
   </when>
   <when value="metadata">
     <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values" 
            help="metadata has the same number of rows as the samples, but the column(s) are floats that describe the samples (e.g. temperature, weight, etc.)"/>
   </when>
  </conditional>
  <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson" >
    <option value="pearson" selected="true">pearson</option>
    <option value="spearman">spearman</option>
    <option value="kendall">kendall</option>
  </param>
  <param name="numaxes" type="integer" value="3" label="numaxes - Number of axes to use (default 3)"/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="axes" name="corr_axes" label="${tool.name} on ${on_string}: corr.axes"/>
 </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 corr.axes_ command calculates the correlation of data to axes.

.. _corr.axes: http://www.mothur.org/wiki/Corr.axes


 </help>
</tool>