view mothur/tools/mothur/chimera.pintail.xml @ 1:fcc0778f6987

Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository

<tool id="mothur_chimera_pintail" name="Chimera.pintail" version="1.16.0">
 <description>Find putative chimeras using pintail</description>
 <command interpreter="python">
  mothur_wrapper.py 
  --cmd='chimera.pintail'
  ## --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.pintail\.chimeras$:'$out_file,'^\S+\.pintail\.accnos$:'$out_accnos,'^\S+\.freq$:'$out_freq,'^\S+\.quan$:'$out_quantile
  #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  #set results = $results + ["'^\S+\.pintail\.chimeras$:'" + $out_file.__str__]
  #set results = $results + ["'^\S+\.pintail\.accnos$:'" + $out_accnos.__str__]
  --outputdir='$logfile.extra_files_path'
  --fasta=$fasta
  --template=$alignment.template
  $filter
  #if $mask.source == 'default':
   --mask=default
  #elif $mask.source == 'history':
   --mask=$mask.input
  #end if
  #if $conservation.__str__ != "None" and len($conservation.__str__) > 0:
   --conservation='$conservation'
  #else
   #set results = $results + ["'^\S+\.freq$:'" + $out_freq.__str__]
  #end if
  #if $quantile.__str__ != "None" and len($quantile.__str__) > 0:
   --quantile='$quantile'
  #else
   #set results = $results + ["'^\S+\.quan$:'" + $out_quantile.__str__]
  #end if
  #if int($window.__str__) > 0:
   --window=$window
  #end if
  #if int($increment.__str__) > 0:
   --increment=$increment
  #end if
  --result=#echo ','.join($results)
  --processors=2
 </command>
 <inputs>
  <param name="fasta" type="data" format="fasta" label="fasta - Candiate Sequences"/>
  <conditional name="alignment">
   <param name="source" type="select" label="Select Template from" help="">
    <option value="hist">History</option>
    <option value="ref">Cached Reference</option>
   </param>
   <when value="ref">
    <param name="template" type="select" label="template - Select an alignment database " help="">
     <options from_file="mothur_aligndb.loc">
      <column name="name" index="0" />
      <column name="value" index="1" />
     </options>
    </param>
   </when>
   <when value="hist">
    <param name="template" type="data" format="fasta" label="template - Template to align with" help=""/>
   </when>
  </conditional>
  <param name="filter" type="boolean" falsevalue="" truevalue="--filter=true" checked="false" label="filter - Apply a 50% soft vertical filter"/>
  <!-- mask -->
  <conditional name="mask">
   <param name="source" type="select" label="Mask option">
    <option value="">None</option>
    <option value="default">default ecoli mask</option>
    <option value="history">From your history</option>
   </param>
   <when value=""/>
   <when value="default"/>
   <when value="history">
    <param name="input" type="data" format="filter" label="Mask for the template file" help=""/>
   </when>
  </conditional>
  <param name="conservation" type="data" format="freq" optional="true" label="conservation - Template Conserved frequencies"
         help="a file containing the frequency information for your template file to increase speed. Mothur will generate this for you but it takes a long time.">
   <validator type="metadata" metadata_name="columns" />
  </param>
  <param name="quantile" type="data" format="quan" optional="true" label="quantile - Template quantile information"
         help=" file containing the quantiles information for your template file to increase speed. Mothur can generate this for you but it takes a VERY long time.  Note that when you use the filter, mask or mask and filter you need to select the appropriate quantile file. The filter parameter makes the quantile file generated specific to the query set you are analyzing."/>
  <param name="window" type="integer" value="0" label="window - Length of sequence you want in each window analyzed (uses default if &lt; 1)" 
         help="Default is set to 300. Note, changing the window size will require new quantile files to be made."/>
  <param name="increment" type="integer" value="25" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)"
         help="Default is 25. Note, changing the increment will require new quantile files to be made."/>
 </inputs>
 <outputs>
  <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
  <data format="txt" name="out_file" label="${tool.name} on ${on_string}: pintail.chimeras" />
  <data format="accnos" name="out_accnos" label="${tool.name} on ${on_string}: pintail.accnos" />
  <data format="freq" name="out_freq" label="${tool.name} on ${on_string}: pintail.freq" >
   <filter>conservation == None</filter>
  </data>
  <data format="quan" name="out_quantile" label="${tool.name} on ${on_string}: pintail.quan" >
   <filter>quantile == None</filter>
   <!-- The following is not working, need to see if filter param can be referenced -->
   <actions>
    <conditional name="filter">
     <when value="True">
       <conditional name="mask">
        <when value="">
         <action type="format" default="filtered.quan"/>
        </when>
        <when value="default">
         <action type="format" default="filtered.masked.quan"/>
        </when>
        <when value="history">
         <action type="format" default="filtered.masked.quan"/>
        </when>
       </conditional>
     </when>
     <when value="False">
       <conditional name="mask">
        <when value="">
         <action type="format" default="quan"/>
        </when>
        <when value="default">
         <action type="format" default="masked.quan"/>
        </when>
        <when value="history">
         <action type="format" default="masked.quan"/>
        </when>
       </conditional>
     </when>
    </conditional>
   </actions>
  </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 chimera.pintail_ command identifies putative chimeras using the pintail approach.

.. _chimera.pintail: http://www.mothur.org/wiki/Chimera.pintail


 </help>
</tool>