<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 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="fasta" name="input" type="data" label="Fasta File" />
    
    <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="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>
    
    <param name="startPos" type="integer" value="1"/> 


   </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 tool uses Weblogo3_ in Galaxy to generate a sequence logo. The input file must be a fasta file in your current history.

It is recommended for (eg) viewing multiple sequence alignments output from the clustalw tool - set the output to fasta and feed
it in to this tool.

A typical output looks like this

.. image:: ${static_path}/images/rgWebLogo3_test.jpg

----

**Warning about input Fasta format files**

The Weblogo3 program used by this tool will fail if your fasta sequences are not all EXACTLY the same length. The tool will provide a warning
and refuse to call the weblogo3 executable if irregular length sequences are detected.

Fasta alignments from the companion 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**

Weblogo attribution and associated documentation are available at Weblogo3_

This Galaxy wrapper was written by Ross Lazarus for the rgenetics project and the source code is licensed under the LGPL_ like other rgenetics artefacts

.. _Weblogo3: http://weblogo.berkeley.edu/

.. _LGPL: http://www.gnu.org/copyleft/lesser.html

  </help>

</tool>