annotate Codonlogo.xml @ 0:c55bdc2fb9fa

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<tool id="codonlogo" name="Codon Logo" version="3">
  <description>generator for fasta (eg Clustal alignments)</description>
  <command interpreter="python"> 
    codonlogo -F $outformat -s $size -f $input -o $output -t "$logoname" -m $frame -n $stacks
    #if $range.mode == 'part'
    -l "$range.seqstart" -u "$range.seqend"
    #end if
    #if $comp.mode == 'equiprobable'
    --composition 'equiprobable'
    #end if
    #if $comp.mode == 'none'
    --composition 'none'
    #end if
    #if $comp.mode == 'file'
    -R $compfile
    #end if
  </command>
  <inputs>
    <page>
      <param format="txt" name="input" type="data" label="txt" />
      <param name="logoname" label="Title for output Sequence Logo" type="text" size="50" value="" />
      <param name="outformat" type="select" label="Output format for image (or text report)" >
      <option value="png" selected="True">PNG screen quality</option>
      <option value="png_print">High quality printable PNG</option>
      <option value="pdf">PDF</option>
      <option value="jpeg">JPG</option>
      <option value="eps">EPS</option>
      <option value="txt">Text (shows the detailed calculations for each position - no image)</option>
    </param>
    <param name="frame" type="select" label="Frame to view the alignment" >
      <option value="0" selected="True">0</option>
      <option value="1">+1</option>
      <option value="2">-1</option>
      <option value="3">Negative Strand 0</option>
      <option value="4">Negative Strand +1</option>
      <option value="5">Negative Strand -1</option>
    </param>
    <param name="stacks" size="5" type="integer" value="20" label="Number of stacks per line, default 20" />
    <conditional name="range">
        <param name="mode" type="select" label="Include entire sequence (default) or specify a subsequence range to use">
          <option value="complete" selected="true">complete sequence</option>
          <option value="part">Only use a part of the sequence</option>
        </param>
        <when value="complete">
        </when>
        <when value="part">    
           <param name="seqstart" size="5" type="integer" value="1" help="WARNING: Specifying indexes outside the sequence lengths will cause unpredictable but bad consequences!" 
             label="Index (eg 1=first letter) of the start of the sequence range to include in the logo">
           </param>
           <param name="seqend" size="5" type="integer" value="99999" label="Index (eg 75=75th letter) of the end of the sequence range to include in the logo" >
           </param> 
        </when>
    </conditional>
    <conditional name="comp">
      <param name="mode" type="select" label="Select expected composition: auto(default), 'equiprobable', 'none' or supply a file with probabilities">
        
        <option value="equiprobable">equiprobable</option>
        <option value="none">none</option>
        <option value="file">from file</option>
        
      </param>
      <when value="auto">
      </when>
      <when value="equiprobable">
      </when>
      <when value="none">
      </when>
      <when value="file">    
        <param format="txt" name="compfile" type="data" label="File containing the expected composition of the sequence. expected: a file with 64 codons followed by their probability" />
      </when>
      
    </conditional>
    <param name="size" type="select" label="Output CodonLogo size" >
      <option value="large" selected="True">Large</option>
      <option value="medium">Medium</option>
      <option value="small">Small</option>
    </param>
   </page>
  </inputs>
  <outputs>
    <data format="pdf" name="output"  label="${logoname}_output.${outformat}">
       <change_format>
           <when input="outformat" value="png_print" format="png" />
           <when input="outformat" value="png" format="png" />
           <when input="outformat" value="jpeg" format="jpg" />
           <when input="outformat" value="eps" format="eps" />
           <when input="outformat" value="txt" format="txt" />
       </change_format>
    </data>
  </outputs>
  <help>

**Note**

This tool uses CodonLogo in Galaxy to generate a sequence logo from a provided alignment. 
The input file must be an alignment in your current history.
The tool will attempt to read a provided file and if it is unable to it will generate an error.

A typical output looks like this

.. image:: ./static/images/CodonLogoExample.png

----

**Warning about input files**

The  program used by this tool will fail if your alignment files are not all the same length.

Fasta alignments from ClustalW Galaxy tool will work but many other fasta files may cause this tool to fail - please do not file 
a Galaxy bug report - this is a feature of the tool and a problem with your source data - not a tool error - please make certain all your fasta 
sequences are the same length!

----

**Attribution**


This Galaxy wrapper was modified for CodonLogo by David Murphy and is based on the wrapper written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ 

.. _Weblogo3: http://weblogo.berkeley.edu/
.. _LGPL: http://www.gnu.org/copyleft/lesser.html
.. _CodonLogo: http://recode.ucc.ie/CodonLogo 

  </help>

</tool>