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<tool id="kplogo" name="kpLogo" version="1.0">
   <description>for positional k-mer analysis</description>
   <command> 
   
   kpLogo $input $inputtype -o $output -alphabet $alphabet $maxk -startPos $startPos $degenerate -seq $col_seq -weight $col_weight -region $region_start,$region_end     
   #if $background.background_model == '-bg'
-bgfile $background_input
#else
$background.background_model
#end if 
  2> tmp; 
   cp ${output}.most.significant.each.position.pdf $output;
   cp ${output}.pdf $logo_prob;
   cp ${output}.info.pdf $logo_info; 
   cp ${output}.freq.pdf $logo_freq;
   cp ${output}.most.significant.each.position.txt $tab_most;
   cp ${output}.pass.p.cutoff.txt $tab_all;
   
    </command>
  <inputs>
   <page>
    <param format="text" name="input" type="data" label="Input sequences (FASTA or Tabular)" />

    <param name="alphabet" type="select" label="Sequence type: DNA/RNA or Protein" >
      <option value="dna" selected="True">DNA/RNA</option>
      <option value="protein">Protein</option>
      <option value="other">Other (not supported yet)</option>
    </param>
    
    <param name="inputtype" type="select" label="Weighted or Ranked" >
      <option value="" selected="True">Unweighted (FASTA or Tab-delimited) </option>
      <option value="-ranked">Ranked (FASTA or Tab-delimited)</option>
      <option value="-weighted">Weighted (Tab-delimited)</option>
    </param>
    
        
    <param name="col_seq" type="integer" value="1" label="For tabular input, sequence is in this column:"  /> 
    
    <param name="col_weight" type="integer" value="2" label="For tabular input, weight is in this column:"  /> 

    <param name="region_start" type="integer" value="1" label="Starting from position (0 or negative numbers interpreted as distance from the end):"  /> 
    
    <param name="region_end" type="integer" value="0" label="Ending at position (0 or negative numbers interpreted as distance from the end):"  /> 

    
    
    <param name="maxk" type="select" label="k-mer length"
      help="k-mer length">
      <option value="-max_k 4" selected="True">1,2,3,4</option>
      <option value="-max_k 3">1,2,3</option>
      <option value="-max_k 2">1,2</option>
      <option value="-k 4">4</option>
      <option value="-k 3">3</option>
      <option value="-k 2">2</option>
      <option value="-k 1">1</option>
    </param>
    
    <param name="degenerate" type="select" label="Degenerate residual (DNA/RNA only)">
      <option value="-gapped" selected="True">ACGTN, i.e. gapped</option>
      <option value="">None (no degenerate residuals)</option>
      <option value="-degenerate all">all IUPAC residuals: ACGTRYMKWSBDHVN</option>
    </param>
    

 
  <conditional name="background">
    <param name="background_model" type="select" label="Background model (only for unweighted sequences)">
      <option value="" selected="True">Average across all positions in input sequences</option>
      <option value="-shuffle 100,2">Shuffle each input sequence 100 times preserving di-residual frequency</option>
      <option value="-markov 1">Markov model learned from input sequences, first order</option>
      <option value="-bg">Background sequences</option>
    </param>
        <when value="-bg">    
               <param format="text" name="background_input" type="data" label="Background sequences (FASTA or Tabular)" />
        </when>
  </conditional>
   

    
    <param name="startPos" type="integer" value="1" label="Redefine position 1. The positions before it will be numbered as -1, -2, etc (no 0)." /> 

    <param name="fix" type="float" value="0.75" label="Fixation frequency"/> 

   </page>
  </inputs>
  <outputs>
    <data format="pdf" name="logo_info" label="${tool.name} on ${on_string}: info"/>
    <data format="pdf" name="logo_freq" label="${tool.name} on ${on_string}: freq"/>
    <data format="pdf" name="logo_prob" label="${tool.name} on ${on_string}: prob"/>
    <data format="pdf" name="output" label="${tool.name} on ${on_string}: kmer"/>
    <data format="tabular" name="tab_all" label="${tool.name} on ${on_string}: all_kmer"/>
    <data format="tabular" name="tab_most" label="${tool.name} on ${on_string}: most_sig"/>


  </outputs>
  <help>

**Note**

This is a wrapper for the positional k-mer analysis tool kpLogo_, which is also available as a web server and stand-alone command-line tool. Please refer to the manual_ on the web server for help information.

To run kpLogo on local Galaxy instances, one needs to compile and install kpLogo locally. Please refer to the web server for details (click here_). 

----


.. _kpLogo: http://kplogo.wi.mit.edu/

.. _manual: http://kplogo.wi.mit.edu/manual.html
  
.. _here: http://kplogo.wi.mit.edu/manual.html#install-kpLogo-locally


  </help>

</tool>